Database of Microbial Interactions (DoMI)

DoMI is an ongoing effort to catalog instances and mechanisms of microbe-microbe interactions found in the literature. Search options allow investigating a variety of attributes (from interacting species to the environment and conditions). If you have any questions or suggestions, please feel free to contact us (www.momenilab.org/contact)!

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SourceLinkType of InteractionSpecies 1Species 2Characterization EnvironmentSpatial ContextAssociation ContextCharacterization Culture ConditionOxygen AvailabilityNative EnvironmentNatural or Engineered?Interaction Identification MethodInteraction MechanismRaw Data Available?NotesContributorCurator
Biogeography of a human oral microbiome at the micron scale, Welch et. al., Proc. Nat. Acad. Sci. USA; https://doi.org/10.1073/pnas.1522149113 Mixed/Commensalism. Streptococcus found to interact specifically with corynebacterium by adhesion. Corynebacterium Streptococcus Spatial; Fixed samples from in vivo human host Biofilm; dental palque in situ; Fixed for fluorophore analysis detailed in Materials and Methods in article; Originally from in vivo sample. aerobic; anaerobic; both aerobic and anaerobic depending on the section of plaque (Detailed diagram in fig. 9). Human oral microbiota Natural imaging; Fluorophore specific to each species Hypothosized to be both for structural stability as well as possible metabolic advantage. Pictures of structures included in article (Link provided) Nick Favazza Babak Momeni
Biogeography of a human oral microbiome at the micron scale, Welch et. al., Proceedings of the National Academy of Sciences of the USA Mixed/Commensalism. Actinomyces (including various Rothia species) found to interact specifically with corynebacterium by adhesion. Actinomyces provides biofilm surface on teeth that corynebacterium can attach "roots" to and expand outward into branches. Corynebacterium Actinomyces Fixed sample from human mouth Fixed samples from in vivo human host Biofilm, dental palque, "corncob structure" described in article. Fixed for fluorophore analysis detailed in Materials and Methods in article. Originally from in vivo sample. Both aerobic and anaerobic depending on the section of plaque (Detailed diagram in fig. 9). Human oral microbiome Natural Fluorophore specific to each species Hypothosized to be primarily structural/spatial arrangement. Pictures of structures included in article (Link provided) Nick Favazza Peter Brand
Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization, Iwase et al. (2010), Nature, doi: 10.1038/nature09074 Amensalism. Esp-secreting S.edidermidis has been shown in vivo to eliminate S. aureus nasal colonization. Firmicutes, staphylococcus, S. epidermidis, strains = JK16, JK11 Firmicutes, staphylococcus, S. aureus, JCM2874, MRSA, MSSA, Mu50, TI1 isolates from human nasal cavities and used for epidemiological and in vivo studies, cultured in lab solid, well-mixed biofilm batch culture conditions, given certain nutrients in culture to see growth aerobic human nasal cavity S. epidermidis was natural from subjects, S. aureus isolated naturally from wound or nasal cavity plating/culturing on media, protein purification, in vivo use of strains, biofilm was measured spectrophotometrically, interaction was confirmed with mutants and complementation Esp secreted by S. epidermidis is hypothesized to inhibit biofilm formation and nasal colonization by S. aureus no Erin Desrocher Kelsey Hyland 09/27/2018 10:37:25 pm
Escherichia coli O157:H7 Survival and Growth on Lettuce is Altered by the Presence of Epiphytic Bacteria, Cooley et al., Journal of Food Protection, 2006 Competition (on foliage, rhizosphere and plant exudate) E. coli O157:H7 Enterobacter asburiae (RM5018) lettuce leaves and isolates also from A. thaliana (ecotype Col-0) solid, well-mixed, 1:1 ratio biofilm in situ; bacterial suspensions pipetted directly onto exposed roots of lettuce. Lettuce seeds were also imbibed and inoculated with strains by tumbling seeds in bacterial suspension. aerobic plants natural- can be found naturally on plant leaves (can be isolated from the species of plant A. thaliana) microscopic examination of coinculated lettuce seeds/leaves via GFP labelling. Observing the growth in plant exudate. available nutrients (rather than space) is thought to be the major factor related to competition- E. coli being forced to colonize a suboptimal niche for survival- involves a diffusible factor that is less available in the subobtimal niche. Initial bindin No raw data available the notes given by the curator were extrememly helpful- adding specific strain information and elaboration on the methods of isolation and detection of interaction (these contributions were added to my submission). Margaret DuChene 09/27/2018 10:37:25 pm John Botzler, Erin Desrocher 09/27/2018 10:37:25 pm
Escherichia coli O157:H7 Survival and Growth on Lettuce is Altered by the Presence of Epiphytic Bacteria, Cooley et al., Journal of Food Protection, 2006 Commensalism (only foliage, not present on plant exudate or rhizosphere). E. coli O157:H7 Wausteria paucula (RM5019) lettuce leaves and isolates also from A. thaliana (ecotype Col-0) solid, well-mixed, 1:1 ratio biofilm in situ; bacterial suspensions pipetted directly onto exposed roots of lettuce. Lettuce seeds were also imbibed and inoculated with strains by tumbling seeds in bacterial suspension. aerobic plants natural- can be found naturally on plant leaves (can be isolated from the species of plant A. thaliana) microscopic examination of coinculated lettuce seeds/leaves via GFP labelling. Observing the growth in plant exudate. commensalism with W. pacula may not involve a diffusible factor since commensalism was not observed in the plant exudate - thought to assit E. coli survival by modifying tissue and supplying a suitable niche (i.e. the release of nutrients from the plant o No raw data available The notes given by the curator were extrememly helpful- adding specific strain information and elaboration on the methods of isolation and detection of interaction (these contributions were added to my submission). Margaret DuChene 09/27/2018 10:37:25 pm John Botzler, Erin Desrocher 09/27/2018 10:37:25 pm
Role of hydrogen peroxidein competitionand cooperation between Streptococcus gordonii and Actinomyces naeslundii. Jakubovics et al. 2008. FEMS microbial ecology. https://doi.org/10.1111/j.1574-6941.2008.00585.x; Mixed; amensalism; commensalism Streptococcus gordonii DL1 (Challis) Actinomyces naeslundii MG1 (ATCC43146) Cultures of type strains Liquid; well-mixed planktonic batch aerobic oral biofilms laboratory strains used (both) plate enumeration Inhibition by hydrogen peroxide; protection by arginine No Babak Momeni 09/27/2018 10:37:25 pm
The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts, Ainsworth et. al 2015, The ISME Journal, doi:10.1038/ismej.2015.39 mutualism coral (species: Acropora granulosa, Montipora capitata, Leptoseris) Actinobacteria: Propionibacterium, Ralstonia, (found within dinoflagellates within coral cells) three different coral species samples collected from natural habitat in the Great Barrier Reef and Hawaiin Archipelagos; DNA then extracted using the MioBio Plant DNA extraction kit; bacterial 16 S rRNA genes then PCR amplified; coral species manipulated coral samples crushed and homogenized (coral holobiont, symbiotic tissue community, and endosybiotic community combined), FFPE (formalin-fixed paraffin- embedded) samples used for tissue sampling Actinobacter and Ralstonia found within dinoflagellates within coral host cell; planktonic in situ; fluorescence in situ hybridization (FISH) not mentioned Great Barrier Reef and Hawaiian Archipelagos natural, coral species isolated from their natural habitats predictive metagenomic analysis nitrogen fixation, metal ion metabolism, significant metabolic exchange between coral host and endosybiotic bacteria (evidence shown by ABC transporters, sugar transporters, permeases, ion couple and general transporter genes), amino-acid metabolism yes, localization of Actinboacter and Ralstonia within endosymbiotic dinoflagellates cells of coral host shown using FISH, dendograms also provided (https://www.nature.com/articles/ismej201539.pdf) comparison across coral species and regions shows consistent, specific interactions do occur Corals harbor highly diverse and abundant microbial communities (estimates upwards of several thousand), but the coral core microbiome consists of sustainably lo Kelsey Hyland 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
Beaudoin, T., Yau, Y. C. W., Stapleton, P. J., Gong, Y., Wang, P. W., Guttman, D. S., & Waters, V. (2017). Staphylococcus aureus interaction with Pseudomonas aeruginosa biofilm enhances tobramycin resistance. Npj Biofilms and Microbiomes, 3(1). Mutualism, synergistic. Polymicrobial interaction causes resistance to antibiotic tobramycin Staphylococcus aureus Pseudomonas aeruginosa static slide chamber model with confocal microscopic visualization liquid biofilm batch both are facultative anaerobes, grown in aerobic conditions Airways of pediatric patients with cystic fibrosis Natural, isolated from CF patients Staining, static slide chamber model with confocal microscopic visualization, image analysis using Volocity and COMSTAT software Psl (exopolysaccharide) produced by P. aeruginosa and staphylococcal protein A from S. aureus bind to promote biofilm growth and tobramycin resistance Yes. See figures and tables in link. .... Quentin Bet 09/27/2018 10:37:25 pm Gabby DeBartolomeo 09/27/2018 10:37:25 pm
Cao M, Patel T, Rickman T, Goodrich-Blair H, Hussa EA. High Levels of the Xenorhabdus nematophila Transcription Factor Lrp Promote Mutualism with the Steinernema carpocapsae Nematode Host. McBain AJ, ed. Applied and Environmental Microbiology. 2017;83(12) Mutualistic and Pathogenic (Mixed); X. nematophila with high-Lrp expression have mutualistic relationships. X. nematophila with low-Lrp expression have pathogenic relationships Xenorhabdus nematophila Steinernema carpocapsae in vitro on agar plates; in vivo (in nematodes and in insects) liquid; well-mixed (coinjections) biofilm in vivo: continuous, bacteria injected into nematode; in vitro: batch, aposymbiotic IJs were surface sterilized and seeded onto the bacterial lawns both are facultative anaerobes, grown in aerobic conditions Found within insect-parasitizing nematodes Engineered for low and high Lrp expression levels plating; microscopic examination mutualistic interaction: aids the nematode in infection of insects (reproduction) No Data from this paper shows that X. nematophila has a mutualistic relationship with nematodes if the bacteria has high Lrp (transcription factor) expression levels Connor Monahan 09/27/2018 10:37:25 pm Gabby DeBartolomeo 09/27/2018 10:37:25 pm
Shanshan Li, Xiaoyu Yu, Wenjuan Wu, Daniel Z. Chen, Ming Xiao, Xinhua Huang,The opportunistic human fungal pathogen Candida albicans promotes the growth and proliferation of commensal Escherichia coli through an iron-responsive pathway,Microbiological Res Commensalism Candida albicans Escherichia coli Normally interacts within the GI tract; Experimental setting is in vitro cultures on agar plates Investigated in both liquid and solid mediums; spatial (strains were grown adjacent to one another) biofilm batch facultatively anaerobic human gastrointestinal tract Engineered plating; examining growth using Thermo Multiskan spectrophotometer; other interactions determined through photographs C. albicans facilitates E. coli cell division No Connor Monahan 09/27/2018 10:37:25 pm Isabel Brandenburger, Quentin Bet 09/27/2018 10:37:25 pm
Experimental evidence of a tripartite mutualism: bacteria protect fungus gardens from specialized parasites, Currie, Bot, and Boomsma 2003, OIKOS, doi: 10.1034/j.1600-0706.2003.12036.x tripartite mutualism actinomycete on Acromyrmex octospinosus escovopsis infection on fungus gardens Fixed A. octospinosus colonies collected from natural habitat in Gamboa and Panama and were maintained, prior to the experiments, in the lab in plastic boxes with one fungus garden, later isolated to agar plates with fungus and bramble leaves; sub-colonie natural habitat simulated in lab using climate room, colonies collected with natural growth of actinomycetes on Acromyrmex octospinosus, fungus garden biomass kept relatively stable and transferred and isolated on solid nutrient agar, Escovopsis infection actinomycete biofilm on Acromyrmex laterocervical plates and back continuous; ants collected from natural habitat, maintained feeding bramble leaves, then placed in fixed stable fungus gardens located on agar with bramble leaves not mentioned Gamboa and Panama; the actinomycete is usually carried on the cuticle of fungus-growing ants actinomycete growth on Acromyrmex octospinosus natural,escovopsis infection engineered in lab dissecting microscope used to determine abundance of actinomycete, logistic analysis (JMP), three- or two- way ANOVA (SYSTAT) depending on experiment, fungus garden weight measured at beginning and end of experiment actinomycete suppresses growth of parasite Escovopsis within A. Octospinosus fungus gardens, actinomycete produces antibiotics in vitro that target pathogen Escovopsis yes; link provided Kelsey Hyland 09/27/2018 10:37:25 pm Connor Monahan 09/27/2018 10:37:25 pm
Rao, D., Webb, J. S., & Kjelleberg, S. (2005). Competitive Interactions in Mixed-Species Biofilms Containing the Marine Bacterium Pseudoalteromonas tunicata. Applied and Environmental Microbiology, 71(4), 1729–1736. Competative inhibition (Pseudoalteromonas tunicata inhibits growth of other bacteria) Pseudoalteromonas tunicata Various epiphytic marine bacteria that grow on Ulva Lactuca: Pseudoalteromonas gracilis, Alteromonas sp., Cellulophaga fucicola, and Roseobacter gallaeciensis continuous-culture flow chambers at room temperature Multispecies biofilm, 1:1 ratio (4:1 and 2:1 for C. fucicola and Alteromonas, respectively) biofilm continuous culture Not mentioned. Surface of the marine algae, U. lactuca surface ; P. tunicata is often found on the surfaces of eukaryotes Competition occurs naturally. Strains were isolated from U. lactuca and grown in vitro. fluorescein isothiocyanate and tetramethyl rhodamine isocyanate optical filters on confocal laser scanning microscope (Olympus) Antibacterial protein (AlpP) serves as extracellular inhibitory compound for P. tunicata during competiton. Microcolonies provide competative advantage. Yes, see figures/tables in link provided ... Quentin Bet 09/27/2018 10:37:25 pm Connor Monahan 09/27/2018 10:37:25 pm
Competition and Coexistence between Streptococcus mutans and Streptococcus sanguinis in the Dental Biofilm Competition Streptococcus mutans Streptococcus sanguinis anaerobic BHI plates of varying environmental conditions to mimic the environment in vitro solid; spatial biofilm batch both facultative anaerobes Human dental mucosal surface natural plating, observation of species growth in the presence of the other species production of inhibitory substances , S. sanguinis produces H2O2 to inhibit the growth of S. mutans Yes, pictures and data in link provided, pg. 7197-9 Gabby DeBartolomeo 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
Immune gene transcription in Drosophila adult flies infected by enteomopathogenic nematodes and their mutualistic bacteria. Journal of Insect Physiology Vol. 59: 2. https://doi.org/10.1016/j.jinsphys.2012.08.003 Cooperation/mutualism Photorhabdus luminescens Heterorhabditis bacteriophora Bacterium P. luminescens cultured in LB broth. H. bacteriophora grown in wax moth larvae, then isolated and prepped on selective media. Injection of P. luminescens (with or without H. bacteriophora) into isolated drosophila. liquid, well mixed suspension Unclear but predicted to be planktonic (?) Batch, in vivo; bacteria and nematodes injected into living drosophila (in a lab setting) P. luminescens: anaerobic, H. bacteriophora: aerobic Usually found within soil nematodes (H. bacteriophora) that infect many types of insect larvae. natural assays created to suspend P. luminescens and H. bacteriophora in drosophila, then RT-PCR used to check for amplification of certain genes/transcription factors P. luminescens secrete toxins and interfere with insect immune response, allowing H. bacteriophora to grow and flourish in dying insect. P. luminescens lives within H. bacteriophora in the wild. No This bacteria allows H. bacteriophora (nematodes) to infect and kill insects. Without the P. luminescens, insects can usually fight off the nematodes with their immune system, but the P. luminescens affects the host insect's gene transcription so that it Lauren Bynum 09/27/2018 10:37:25 pm Peter Brand 09/27/2018 10:37:25 pm
Interactions between lactobacillus kefiranofaciens and Saccharomyces cerevisiae in mixed culture for kefiran production. Journal of Bioscience and Bioengineering Vol. 96:3. https://doi.org/10.1016/S1389-1723(03)80194-9 Commensalism (L. kefiranofaciens benefits while S. cervisiae not affected) Lactobacillus kefiranofaciens Saccharomyces cerevisiae seed cultures of L. kefiranofaciens and S. cerevisiae were inoculated into a jar fermentor liquid - both well mixed and pure cultures were grown biofilm Batch cultures L. kefiranofaciens and S. cerevisiae: facultative anaerobes, grown here anaerobically Inside kefir grains; L. kefiranofaciens obtained from the Japan Collection of Microorganisms, Wako and S. cerevisiae obtained from a collection from the Institute of Fermentation Osaka, Osaka It can occur naturally but this specific culture community was created via various lab strains being mixed together. Amount of kefiran measured both with and without presence of S. cerevisiae via colorometric quantification (observing optical density and comparing the standard curve of lactose optical density).; Hydrogen peroxide conc. and total kefiran production by L. Interaction mechanism was most likely that physical contact between the two bacteria stimulates growth and kefiran production by L. kefiranofaciens in a mixed culture, as S. cerevisiae induces L. kefiranofaciens to produce more lipid carriers in the cell No If this mechanism of interaction is more thoroughly researched, it can be used to improve kefir production for milks and yogurts! Lauren Bynum 09/27/2018 10:37:25 pm Ryann Gutierrez 09/27/2018 10:37:25 pm
Streptococcus mutans Competence-Stimulating Peptide Inhibits Candida albicans Hypha Formation Competition Streptococcus mutans Candida albicans plates with 70% yeast nitrogen base (YNB) and 30% brain heart infusion (BHI) or blood agar, saliva present to mimic the environment of the human oral cavity solid biofilm batch cultures S. mutans is a facultative anaerobe, C. albicans is an aerobic yeast; performed in aerobic environment human oral microbiota natural plating observation S. mutans secretes one or more diffusable substances that prevent C. albicans hyphae formation, one such molecule is CSP (shown to prevent hyphae formation in this experiment), and another potential inhibiting substance is AI-2 (for future experiments) raw data provided in the paper Possible that there are additional molecules that are released by S. mutans to inhibit hyphae formation, but this paper dealt mostly with CSP Gabby DeBartolomeo 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
S. E. GILLILAND and M. L. SPECK (1977) Antagonistic Action of Lactobacillus acidophilus Toward Intestinal and Foodborne Pathogens in Associative Cultures. Journal of Food Protection: December 1977, Vol. 40, No. 12, pp. 820-823., https://doi.org/10.4315/03 ammensalism Lactobacillus acidophilus (strains NCFM, 4962, CNRZ 216, CNRZ 218, HA3, HM6) Staphylococcus aureus B925 Several types of media used to provide adequate nutrients for associative cultures; Strains cultured in lactobacilli MRS broth; MRS broth plus .5% sodium thoglycollate; 10% NFMS plus .5% thiotone; and 10% NFMS plus .5% yeast extract Liquid, well-mixed planktonic continuous anerobic human intestinal tract and food Usually occur naturally but these strains were obtained from the Food Science Department in North Carolina and the E. coli was collected from the Food and Drug Administration Selective plate media used to determine the number of CFU (colony-forming units) of pathogens per mL and therefore the % inhibition of S. aureus (S. aureus found to be 96.8% inhibited by Lactobacillus); titration used to measure pH consumption of Lactobacillus acidophilus hypothesized to produce inhibitory effects on enteric pathogens and can be used to treat patients yes, link provided hydrogen peroxide is only responsible for a small portion of antagonist activity; gram positive bacteria (S. aureus and C. perfingens) were more sensitive to the inhibitory action than gram negative species (S. typhimurium and E. coli) Jaimie Kirkpatrick 09/27/2018 10:37:25 pm Kelsey Hyland, Quentin Bet 09/27/2018 10:37:25 pm
Microbe–microbe interactions trigger Mn(II)-oxidizing gene expression cooperation actinobacteria, micrococcaceae, Arthrobacter, strain QXT-31 proteobacteria, Sphingopyxis, strain QXT-31 isolates from soil surface at Xiangtan manganese mine co-cultured in lab well-mixed in liquid planktonic batch aerobic soil strains of these species are found naturally in soil and were taken from the environment to use in the lab co-culturing methods, BN-PAGE, in-gel Mn(II) oxidation assay, gene sequencing, serial dilution plating Arthrobacter contains a coding gene that expresses an Mn(II) oxidizing protien but requires sustained contact with the metabolically active Sphinogopyxis cells to do so no Erin Desrocher 09/27/2018 10:37:25 pm Jaimie Kirkpatrick 09/27/2018 10:37:25 pm
Pseudomonas-Candida Interactions: An Ecological Role for Virulence Factors Deborah A. Hogan, Roberto Kolter ammensalism Pseudomonas aeruginosa (bacterium) Candida albicans (fungus) (yeast form and filamentous cells) cultured together to observe attachment of bacteria (P. aeruginosa) to fungus (C. albicans) in its yeast form or filamentous form mixed minimal solid media biofilm continuous not specified Pseudomonas aeruginosa: soils and on skin/mucosa of healthy individuals; Candida albicans: skin and mucosal flora natural plate count assays, phase-contrast imaging, microscopic examination interactions between P. aeruginosa and C. albicans can reflect the relationships of bacterial and fungal species that coexist in other environments and show the the role of known virulence determinants that could lead to discovery of new factors involved yes, link provided Jaimie Kirkpatrick 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
Guo, F., Wu, Z., Ye, C., Yu, X., Zhang, S. (2012). Evidence for Broad-Spectrum Biofilm Inhibition by the bacterium Bacillus sp. Strain SW9. Applied and Environmental Microbiology, 79. doi:10.1128/AEM.02796-12 ammensalism in the form of biofilm inhibition Bacillus sp. strain SW9 Thauera sp. GS2 in vitro; on solid agar plates. Thauera sp. GS2 obtained from water sample and isolated. solid, well-mixed biofilm continuous culture Conditions not specified but most likely aerobic conditions Bacillus sp. SW9 isolated from a drinking-water source. Thauera sp. GS2 was isolated from granule sludge source. Natural. Bacillus sp. SW9 was isolated from a drinking water source and Thauera sp. GS2 was isolated from granule sludge source. plating assays for biofilm formation using a 96-well microtiter plate and a 24-well plate incubated 24-72 hours , Scanning Electron Microscpopy (SEM) Bacillus sp. strain SW9 responsible for inhibition via direct cell-to-cell contact or in combination with secreted inhibitory compounds. Fimbrial repression considered to be responsible for biofilm inhibition. yes, found in the link provided John Botzler 09/27/2018 10:37:25 pm Margaret DuChene 09/27/2018 10:37:25 pm
Kuramitsu, H. & Wang, B. (2005) Interactions between Oral Bacteria: Streptococcus mutans Bacteriocin Production by Streptococcus gordonii. Applied and Environmental Microbiology, 71. doi: 10.1128/AEM.71.1.354-362.2005 ammensalism Streptococcus mutans (strains B5 and GM71) Streptococcus gordonii Challis Streptococcus gordonii (strain= challis) in vitro; on solid agar plates, bacteria also routinely cultured in Todd-Hewitt broth. solid and liquid, well mixed biofilm; dental plaque continuous culture aerobic human oral microbiota natural plating assays, agar well assays, killing assays. used RP66, a group C streptococcal strain, as an indicator strain. S. gordonii (Challis) knockout created via double crossover and transformation, zymography of supernant fluids from S. gordonii and mutan S. mutans bacteriocin production is inhibited by the S. gordonii production of challasin protease via the sgc gene. The inhibition of bacteriocin production prevents the further growth of the S. mutans. yes, found in the link provided John Botzler 09/27/2018 10:37:25 pm Margaret DuChene 09/27/2018 10:37:25 pm
Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species commensalism Staphylococcus aureus Corynebacterium striatum cultured in Brain Heart Infusion broth or solid agar; combination of both; samples from human nasal cavities mixed; combination of solid and liquid media for culturing planktonic batch culture conditions; testing between mono- and co- cultures for different gene expressions aerobic human nasal cavity natural DNA and RNA sequencing hypothesized to be a transcriptional change is S. aureus making it no longer a pathogen yes; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988121/#SM1 Isabel Brandenburger 09/27/2018 10:37:25 pm Jaimie Kirkpatrick 09/27/2018 10:37:25 pm
Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP. Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols. mBio. 2016;7(1):e01725-15. doi:10.1128/mBio.01725-15. inhibition Corynebacterium accolens Streptococcus pneumoniae solid agar supplemented with catalase solid; spatial biofilm; pediatric nasal passages batch culture Grown in aerobic conditions- S. pneumoniae is facultative anaerobe, C. accolens is aerobic nasal passages particularly of prepubescent children natural liquid chromatography/mass spectometry analysis of C. accolens methanol extracts to determine the compounds in the zones of inhibition hydrolysis of triolein by C. accolens releases oleic acid into the environment, which inhibits the growth of S. pneumoniae through membrane depolarization and cell rupture yes in link provided Isabel Brandenburger 09/27/2018 10:37:25 pm Lauren Bynum 09/27/2018 10:37:25 pm
Zhou F., Lou Q., Wang B., Xu L., Cheng C., Lu M., Sun J., Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis; doi:10.1038/srep20135 competition Leptographium procerum Ophiostoma minus culture on phloem media; fungus colonized phloem media in presence or absence of bacteria on RTB larval growth solid; spatial biofilm batch culture anaerobic gut microbiota of red turpentine beetle natural phylogenetic analysis followed by plating on phloem media competition for carbohydrates by inhibiting D-glucose consumption of O. minus yes, see data from link Peter Brand 09/27/2018 10:37:25 pm Ryann Gutierrez 09/27/2018 10:37:25 pm
Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot. commensalism Salmonella enterica serovar Typhimurium Pectobacterium carotovorum cultured in xylose lysine deoxycholate (XLD) agar at 42 degrees Celsius solid; spatial biofilm batch culture anaerobic tomato soft rot natural plating on XLD agar and transposon insertion analysis P. carotovorum gives S. Typhimurium a metabolic advantage brought on by csrBC small regulatory RNA no Peter Brand 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
Variability and interactions between endophytic bacteria and fungi isolated from leaf tissues of citrus rootstocks; Welington L. Araujo, Walter Maccheroni Jr., Carlos I. Aguilar-Vildoso, Paulo A.V. Barroso, Halha O. Saridakis, and Joao Lucio Azevedo; Cana commensalism, mutualism, inhibition bacterial species included Bacillus cereus, Bacillus lentus, Bacillus megaterium, Bacillus pumilus, and Bacillus subtilis, Burkholderia cepacia, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium extorquens, and Pantoea agglomerans fungal species included Colletotrichum gloeosporioides, Guignardia citricarpa, and Cladosporium fungi isolated endophytically from healthy citrus plants; bacteria isolated from xylem of lemon roots; plants came from Instituto Agronomico de Campinas in Sao Paulo Brazil. Interactions tested both on LB agar plates and in LB broth solid ( TSA and CMA); liquid biofilm ? (not clear) insitu? fungi/ bacteria isolated from leaves/seeds of citrus plants; batch ? (not clear) aerobic surface leaf tissues of citrus plants/ rootstocks natural See materials/ methods for more detail; bacterial density measured on leaf and seed fragments, the endophyte incidence (EI) was calculated; DNA extraction( bacteria grown in LB broth); each strain went though RAPD analysis, PCR, gel; difference of total certain bacteria/ fungi only found in certain areas of the citrus fruit; as found some could not co exist with eachother; analyzed ecological niche; some endophytes favored as biocontrol agents and exhibit potential as a gents against pathogens, insects, no endophytic-microrganisms that reside in the same life cycle within a living plant tissue; isolated endophytic fungi and fast growinfg endophytic fungi to characteruze interactions on citrus plants; interaction between bacteria and Guignardia citricarpa ( Ryann Gutierrez 09/27/2018 10:37:25 pm Lauren Bynum 09/27/2018 10:37:25 pm
Metabolic activity and symbiotic interactions of lactic acid bacteria and yeasts isolated from water kefir; Jasmin Stadie, Anna Gulitz, Matthias A. Ehrmann, Rudi F. Vogel; ELSEVIER Food Micorbiology mutualism lactic acid bacteria:Lactobacillus hordei, Lactobacillus nagelii yeasts: Zygotorulaspora florentina, Saccharomyces cerevisiae water kefir organisms, isolated and characterized by Gulitz et al. (2011); ;lactobacilli were precultured in MRS medium and yeasts in YPG medium; experiemnts occured in water kefir medium Corning Transwell culture system liquid as well solid planktonic? (not clear) batch anerobic in water kefir environments in experiment various lab strains were interacted together, but bacterial/yeat interactions can also occur naturally see materials/ methods for more detail; experiments occured in water kefir environment, co-cultivation occured using Corning Transwell culture system; essential nutrients of water kefir isolates were identified in SCDM; used 2 different concentrations of lactobacilli acidify medium increasing yeast growth; yeasts produce essential nutrients for growth ( amino acids and vitamins) of lactobacilli no water kefir is a sour alcoholic drink fermented by multiple microbes in a community; it is a co-culture model system; co cultivation of lactobacilli and yeasts in WKM increases cell yeild; study aims to understand the type of interactions between micro Ryann Gutierrez 09/27/2018 10:37:25 pm Erin Desrocher 09/27/2018 10:37:25 pm
Coexisting Curtobacterium Bacterium Promotes Growth of White-Rot Fungus Stereum commensalism Stereum sp. TN4F Curtobacterium sp. TN4W-19 isolates from fallen wood bark, cultured in lab setting on R2A medium solid, well mixed biofilm batch aerobic forest ecosystems natural isolation with selective plating, confrontational assay of fungus and bacterial isolates, bacterial and fungal DNA isolation with ISOPLANT and sequencing; PCR to amplify 16S rRNA gene of bacterial DNA and 5.8S rRNA gene of fungal DNA Curtobacterium was found to improve mycelial growth of the white-rot fungus Stereum no Erin Desrocher 09/27/2018 10:37:25 pm Jaimie Kirkpatrick 09/27/2018 10:37:25 pm
Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans competition Candida albicans: strains SC5314, DHC271, CEGC1 Enterococcus faecalis: strains OG1RF, TX5266, CK111, CEGF1, CEGF2 biofilms were assayed on artificial saliva media solid, well mixed biofilm batch aerobic GI tracts, oral cavity, and urogenital tract of humans and other mammals natural in vitro model was created with artificial saliva media, microscopic imaging of biofilms, quantitations of biomass of biofilms E. faecalis potentially inhibits biofilm growth by preventing switch to the hyphal form, and this leads to a decreased virulence and biofilm formation of C. albicans cells no Erin Desrocher 09/27/2018 10:37:25 pm Jaimie Kirkpatrick 09/27/2018 10:37:25 pm
The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescensPf29Arp commensalism Gaeumannomyces graminis var. tritici (Ggt) isolate IV‐26/00 P. fluorescens Pf29Arp isolates from wheat roots, bacteria grown on solid media and then suspended in the liquid yeast culture solid and liquid, well mixed biofilm batch aerobic soil and roots of plants natural Ggt was stored on potato dextrose agar, P. fluorescens was stored in glycerol nutrient broth, in vitro bioassay was created on solid complete medium, DNA isolation and sequencing, fluorescent imaging of microarrays, quantitative-RT PCR Ggt increased the growth rate of P. fluorescens and induced bacterial genes involved in mycelium colonization, genes encoding protein of stress response and patatin-like protein were up-regulated no Erin Desrocher 09/27/2018 10:37:25 pm Jaimie Kirkpatrick 09/27/2018 10:37:25 pm
Influenza A Virus-Infected Hosts Boost an Invasive Type of Streptococcus pyogenes Infection in Mice commensalism Streptococcus pyogenes (group A streptococcus, GAS) non-lethal Influenza A virus (IAV) - IAV A/FM/1/47 (H1N1) IAV obtained from Madin-Darby canine kidney (MDCK) cells, a canine kidney epithelial cell line, GAS obtained from K. Kikuchi and K. Totsuka and T. Murai, mice infected intranasally with IAV and then GAS samples from in vivo mouse host planktonic In situ - bacteria and virus placed directly into mouse host aerobic GAS naturally resides in humans, IAV exists within many different hosts engineered To enumerate the number of GAS, the lungs, spleens, livers, and kidneys were dissected and dilutions of each suspensions were plated on THY blood agar plates, Virus numbers were assessed by a focus reduction neutralization test Possible that a mixed infection with the influenza virus and GAS is one of the most essential factors causing outbreaks of invasive GAS diseases. This study used mice hosts in hopes of being able to mimic what occurs in human host No Jaimie Kirkpatrick 09/27/2018 10:37:25 pm Quentin Bet 09/27/2018 10:37:25 pm
Activation of human immunodeficiency virus by herpes simplex virus. commensalism Human immunodeficiency virus (HIV) Herpes simplex virus type 1 (HSV-1) HIV linked to an indicator gene chloramphenicol acetyltransferase (CAT) and transferred to Vero cells with or without trans-activating gene (tat) of HIV. Vero cells grown in mixture of minimal essential medium and 199 medium containing penicillin, strepto In vivo Vero cell host, well-mixed planktonic continuous aerobic? not listed natural For CAT assays, cell extracts were prepared and analyzed by chromatography. For reverse transcriptase assays, reaction mixtures were prepared and underwent autoradiography HSV-1 and its immediate-early genes ICP0 and ICP4 stimulate expression of HIV LTR-directed viral gene expression, measured by the production of CAT. The stimulatory effects of HSV and immediate-early genes show implications for HIV-induced disease, since No Jaimie Kirkpatrick 09/27/2018 10:37:25 pm Quentin Bet 09/27/2018 10:37:25 pm
Herpes simplex virus type 2 modulates the susceptibility of human bladder cells to uropathogenic bacteria commensalism Herpes Simplex Virus type 2 (HSV-2) strain 333 Escherichia coli strain U1 isolated from patient affected by severe hemorrhagic cystitis HSV-2 propagated in Vero cells, E. coli cultured in brain heart infusion broth and subcultured on trypticase soy agar broth, analyzing cultures of virus and bacteria in human bladder carcinoma cell line (HT-1376) Solid, well-mixed planktonic continuous aerobic E. coli found in human GI tract natural After viral-bacterial infection, cell monolayers washed and plated on TSA to determine number of viable intracellular bacteria; used transmission electron microscopy and immunofluorescence Cultures of S. thermophilis and L. bulgaricus produced more acid in mixed than in single strain culture and growth of S. thermophilius in mixed culture was enhanced. L. bulgaricus was inhibited in the exponential phase of growth in mixed culture. L. bulg No Jaimie Kirkpatrick 09/27/2018 10:37:25 pm Quentin Bet 09/27/2018 10:37:25 pm
Insecticidal Bacillus thuringiensis Silences Erwinia carotova Virulence by a New Form of Microbial Antagonism, Signal Interference antagonism, more specifically signal interference B. thuringiensis- 6 strains used E. carotovora SCG1 and SCG1-GFP Potato Slices (Solanum tuberosum) - dipped into a suspension of B. thuringiensis at a concentration of 5 × 108 CFU/mL and then inoculated with E. carotovora SCG1 bacterial suspension at different concentrations. potato slices (solid) (Solanum tuberosum), well-mixed, coinoculation, evenly mixed at varying concentrations biofilm in situ, B. thuringiensis is a soil bacterim while E. carotovora is found on potatos naturally and causes potato soft rot disease aerobic B. thuringiensis is a soil bacterium while E. carotovora is a plant bacterial pathogen. natural and engineered species were used. Potato slices were coinoculated with both bacterial species. Following 20 h of incubation (28 degrees celsius) maceration area was measured at different time points. Also, visual changes in the development of soft rot symptoms on the potato tissue was m B. thuringiensis bacteria interrupts quorum-sensing signaling of E. carotovora when they live as commensals. such signal interference resulted in drastic attenuation of E. carotovora virulence. B. thuringiensis showing AHL-lactonase activity provide preve No Margaret DuChene 09/27/2018 10:37:25 pm John Botzler, Margaret DuChene 09/27/2018 10:37:25 pm
Interspecies competition triggers virulence and mutability in Candida albicans- Pseudomonas aeruginosa mixed biofilms. competition Candida albicans (CAI4) Pseudomonas aeruginosa (PAO1) In vivo- cultures on complete synthetic media to generate mixed and single-species biofilms. solid, well-mixed and single species biofilms created biofilm batch both normoxic and hypoxic conditions were created (using plates wrapped in parafilm for hypoxic conditions and unwrapped for normoxic). Both microbes are commonly isolated from the septum of cystic fibrosis patients and are common non-pathogenic commensals of healthy individuals. (oppurtunisitc pathogens) natural The total population of each speces in the cultures was determined by the number of CFU. Spectrophotometric assys were used to test iron and oxygen quantitation. Whole-Cell proteins were isolated via centrifugation and Percoll gradient and protein extra After 48 h of coculture, the fungal species is killed by the bacterium due to competition for limited resources (specifically iron, which triggersthe expression of iron-regulated virulence factors in P. aeruginosa). It is hypothesized that after the firs No Margaret DuChene 09/27/2018 10:37:25 pm John Botzler, Margaret DuChene 09/27/2018 10:37:25 pm
Commensalism and Competition in Mixed Cultures of Lactobacillus bulgaricus and Streptococcus thermophilus. commensalism and competition. Lactobacillus bulgaricus Streptococcus thermophilus In vivo- broth cultures liquid, mixed cultures (and single cultures to serve as control) planktonic batch aerobic both microbes are commonly added to dairy products to control the production of lactic acid. engineered? Acidity of mixed and pure cultures of L. bulgaricus and S. thermophilus wa measured following different time intervals of incubation and or temperature conditions. No inhibitory factor could be displayed so inhibition of L. bulgaricus is assumed to be due to the competitive and rapid utilization of some essential nutrient by the faster growing S. thermophilus. A competitive growth advantage for S. thermophilus als No Margaret DuChene 09/27/2018 10:37:25 pm John Botzler, Margaret DuChene 09/27/2018 10:37:25 pm
The contribution of bacteriocin to inhibition of Listeria monocytogenes by Carnobacterium piscicola strains in cold-smoked salmon systems. Journal of Applied Microbiology 96(1): 133-143. https://doi.org/10.1046/j.1365-2672.2003.02129.x inhibition, active competition Carnobacterium piscicola (strains A9b, DSM 20730) Listeria monocytogenes (strain O57) Bacteria isolates were analyzed in vacuum packed cold smoked salmon, salmon juice, and BHI broths liquid, well mixed biofilm batch aerobic C. piscicola is common on meats, fish, and dairy (isolated from smoked salmon), while L. monocytogenes is found as a contaminant in many foods and is found on food or in animal GI tracts Natural Cell numbers of L. monocytogenes was measured by using diffusion of liquid in well diffusion assays to compare growth rate when C. piscicola was present and bacteriocin producing and present without bacteriocin production. Plating and zone of inhibitions C. piscicola has a marked antilisterial effect. The mechanism is not exactly known, but it is known that bacteriocin produced by C. piscicola inhibits growth of L. monocytogenes to prevent spoilage, causing L. monocytogenes to go into stationary phase fas No It would be really cool if the mechanism is determined because then we could look into preventing spoilage of meats/contamination with Listeria by using bacteriocin producing organisms like C. piscicola! Lauren Bynum 09/27/2018 10:37:25 pm Erin Desrocher, Lauren Bynum 09/27/2018 10:37:25 pm
Bacteriocin-producing Enterococcus casseliflavus IM 416K1, a natural antagonist for control of Listeria monocytogenes in Italian sausages ("cacciatore"). International Journal of Food Microbiology 87(1-2):173-179. https://doi.org/10.1016/S0168-1605(03)000 Inhibition, competition Enterococcus casseliflavus (IM 416K1 Bac+, IM 416K1 Bac−) Listeria monocytogenes (NCTC 10888) In vitro- E. casseliflavus was isolated form Italian sausages and then new "cacciatore" sausages were made and inoculated with the two microbes. Cultured in both well mixed broth and on spatial agar media so both liquid and solid media. Colonies were then well mixed into cacciatore sausages. biofilm batch Aerobic L. monocytogenes is a food borne pathogen found in many food products and in GI tracts of the infected (can proliferate and survive even at refridgerated temperatures). E. casseliflavus is often found in raw meat products (also found in dairy products) Isolated from natural sources (meat), but strains placed together by researchers. Bacterial counts of each microbe were determined by spread plating suspensions of small amounts of each sausage. L. monocytogenes was inhibited both by natural competition with the E. casseliflavus and by the enterocin that the E. casseliflavus produces. The enterocin works as an antimicrobial preventing full growth of L. monocytogenes, but the mechanism is not comp No Lauren Bynum 09/27/2018 10:37:25 pm Erin Desrocher, Lauren Bynum 09/27/2018 10:37:25 pm
Control of Beef Spoilage by a Sulfide-Producing Lactobacillus sake Strain with Bacteriocinogenic Leuconostoc gelidum UAL187 during Anaerobic Storage at 28C. Applied and Environmental Microbiology 62(7):2610-2614. Leisner, J. J., G. G. Greer, and M. E. Sti Inhibition, competition Lactobacilus sake (strain 1218) Leuconostoc gelidum (strains UAL187, UAL187-22, UAL187-13) In vitro- beef was incoculated with the strains and then vacuum packaged and left to grow. Solid media, well mixed verified biofilm batch anaerobic (vacuum packaged) Both microbes are often found in chilled, stored meat. Lactobacillus sake is also found in other foods such as fish and dairy. Naturally Samples were homogenized in a stomacher and then suspended in peptone water. The samples were then diluted and surface plated onto M5 and MRS agar, incubated for 3 days, and then colony numbers of each micorbe analyzed. The microbes were also incouclated When coinoculated with L. gelidum, L. sake was inhibited by the antimicrobial bacteriocin produced by L. gelidum. Bacteriocin works as an antagonist to L. sake, preventing most of its growth and allowing L. gelidum to have a head start in competition for No Lauren Bynum 09/27/2018 10:37:25 pm Erin Desrocher, Lauren Bynum 09/27/2018 10:37:25 pm
Interactions among lactic acid starter and probiotic bacteria used for fermented dairy products; Vinderola, C G; Mocchiutti, P; Reinheimer, J A. Journal of Dairy Science; Champaign Vol. 85, Iss. 4, (Apr 2002): 721. inhibition Lactobacillus acidophilus Lactobacillus delbrueckii subsp. bulgaricus lactic acid starter bacteria (L. bulgaricus)isolated from commercial strains from 'local industries' and Probiotic strains of Lactobacillus acidophilus were isolated from commercial strains as well as CNRZ collection-INRA, Jouy-en-Josas, France; all str liquid broth; lactic acid bacteria grown in 10% reconstituted skim milk at 37 degrees celcius for 24 hours; probiotic bacteria grown in MRS broth and 10% reconstituted skim milk at 37 degrees celcius for 24 hours; solid agar. Both well mixed liquid broth biofilm batch aerobic Lactobacillus acidophilus is found naturally in the GI tract and mouth; Lactobacillus delbrueckii subsp. bulgaricus is also found naturally in GI tract and is main bacteria used for yogurt production Both found naturally; however interaction is engineered for yogurt production. cell free supernatents were obtained through centrifiugation of overnight cultures and sterilized through filtration and kept frozen: made well-diffusion Agar assays to determine interactions; MRS or Eliliker agar were melted and tempered and mixed with Lactobacillus delbrueckii subsp. bulgaricus inhibited by Lactobacillus acidophilus due to the presence of bacteriocin-like substance produced; possibly that during cold storage of fermented milk Lactobacillus acidophilus can grow and its metabolic wastes no Ryann Gutierrez 09/27/2018 10:37:25 pm Lauren Bynum, Ryann Gutierrez 09/27/2018 10:37:25 pm
Interaction of Streptococcus pneumoniae and Moraxella catarrhalis: Investigation of the Indirect Pathogenic Role of beta-lactamase producing Moraxellae by use of a continuous culture biofilm system'R. K. Budhani and J. K. Struthers; Antimicrobial Agents a commensalism? Streptococcus pneumoniae Moraxella catarrhalis Cultured in vitro in BHI broth and in Sorbarod biofilms, S. pneumoniae ATCC 671310 clinical isolate (serotype 19); M. catarrhalis ATCC 25238 (β-lactamase negative) from departmental teaching stocks; as well as isolates of S. pneumoniae resistant to penic solid; supernatant broth culture biofilm continuous aerobic? M. catarrhalis naturally found in the respiratory tract; S. pneumoniae also found in upper respiratory tract natural Cultured simple Sorbarod continuous culture biofilm using Sorbarod filters and then analyzed by measuring titers of various biofilms on blood agar; biofilms exposed to antibiotics; supernantants of broth culture were read at 492 nm in a Multiscan MCC/340 S. pneumoniae survival in the presence of antibiotics due to M. catarrhalis BRO-1 B-lactamase positive; direct mechanism unsure but it is predicted an interspecies signalling system may be involved when S. pneumoniae is stressed by antibiotics. no Ryann Gutierrez 09/27/2018 10:37:25 pm Lauren Bynum, Ryann Gutierrez 09/27/2018 10:37:25 pm
Furnkranz U, Walochnik J, Henrich B. Mycoplasma hominis shows strain-dependent increase of resistance to selected antibiotics after symbiosis with Trichomonas vaginalis. J Glob Antimicrob Resist. 2018 Apr 13. pii: S2213-7165(18)30070-5. doi: 10.1016/j.jga commensal; selected drug resistance in M. hominis increases in symbiosis with T. vaginalis Mycoplasma hominis Trichomonas vaginalis in vitro in TYM media (Trypticase-Yeast-Maltose) liquid; cultivating the passaging of cells: M. hominis cells were added to T. vaginalis culture not specified, but likely biofilms batch microaerophilic conditions M. hominis from vaginal flora, but also amniotic fluid, umbilical cord blood, and fetal membranes in 20% of preterm newborns; T. vaginalis form the human genital tract natural; Mycoplasma hominis V475 was isolated from a vaginal swab from a healthy woman, AKH136 isolated from the placenta of a woman with preterm delivery, MhSS10 isolated from endosymbiosis with T. vaginalis Analysis of the MIC (minimal inhibitory concentration) of different antibiotics. MIC was determined by the lowest concentration of antibiotics that causes a color change of 10^5 color changing units within 48 hours symbiosis with T. vaginalis has an enhancing effect on selected antiobiotic resistances of distinct M. hominis isolates no whether the effect is an ehancing or decreasing one seems to depend on the genetic repertoire of the M. hominis isolate tested Connor Monahan 09/27/2018 10:37:25 pm Kelsey Hyland, Connor Monahan 09/27/2018 10:37:25 pm
Khare, A., & Tavazoie, S. (2015). Multifactorial Competition and Resistance in a Two-Species Bacterial System. PLoS Genetics, 11(12), e1005715. http://doi.org/10.1371/journal.pgen.1005715 competition Pseudomonas aeruginosa Escherichia coli liquid media experiments were in modified M63 media; for other experiments, bacteria was grown in LB liquid media or on LB plates liquid; well-mixed planktonic batch aerobic E. coli: intenstines; P. aeruginosa: opportunistic pathogen that generally lives in soil and marshes, but is often found in multi-species infections engineered mass spectrometry of spent media; analysis of clones by whole genome sequencing; cell densities were measured for various assays E. coli growth is inhibited/limited by molecuels secreted by P. aeruginosa and by iron limitation by siderophores secreted by P. aeruginosa microarray data available. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72283 Connor Monahan 09/27/2018 10:37:25 pm Isabel Brandenburger, Connor Monahan 09/27/2018 10:37:25 pm
Laganenka, L., & Sourjik, V. (2018). Autoinducer 2-Dependent Escherichia coli Biofilm Formation Is Enhanced in a Dual-Species Coculture. Applied and Environmental Microbiology, 84(5), e02638–17. http://doi.org/10.1128/AEM.02638-17 cooperation Enterococcus faecalis Escherichia coli strains and plasmids grown in liquid tryptone broth liquid; well-mixed biofilm not-specified both facultative anaerobes, cultivated in anaerobic microtiter plates both inhabit the human gastrointestinal tract, co-occur in catheter associated uniary tract infections natural fluorescent labeling of E. faecalis; confocal laser scanning microscopy of statis biofilms; flow cytometry; fluorescence microscopy; hydrogen peroxide treatment AI-2 produced by E. faecalis promotes bioflim formation of E. coli. It also leading to chemotaxis-dependent coaggregation between the species. The mixed species biofilm increases stress resistance yes (the scanning microscopy images are raw data, and those are included in the paper) Connor Monahan 09/27/2018 10:37:25 pm Gabby DeBartolomeo, Connor Monahan 09/27/2018 10:37:25 pm
An D, Danhorn T, Fuqua C, Parsek MR. Quorum sensing and motility mediate interactions between Pseudomonas aeruginosa and Agrobacterium tumefaciens in biofilm cocultures. Proc Natl Acad Sci USA. 2006;103(10):3828-33. Competition Pseudomonas aeruginosa Agrobacterium tumefaciens flow cells in environmental chamber, 30 degrees C liquid biofilm, as well as planktonic continuous flow aerobic freshwater, bulk soil, rhizosphere natural epifluorescence microscopy; confocal laser scanning microscopy and processed with VOLOCITY surface motility, quorum sensing, and biofilm formation are crucial for competition; P.a. blankets immature A.t. microcolonies due to having a higher growth rate No - Quentin Bet 09/27/2018 10:37:25 pm Gabby DeBartolomeo 09/27/2018 10:37:25 pm
Naaber P, Smidt I, Stsepetova J, Brilene T, Annuk H, Mikelsaar M. Inhibition of Clostridium difficile strains by intestinal Lactobacillus species. J Med Microbiol. 2004;53(Pt 6):551-4. inhibition, antagonistic Clostridium difficile various Lactobacillus species in vitro, on agar plates solid, blood agar plates not specified batch anaerobic human intestines natural Toxin A detected by Oxoid Toxin A test; MICs detected by E test; Jandel SigmaStat 2.0 software by using Fisher, Spearman correlation and Mann-Whitney tests. Antagonistic activity seems to be linked to H2O2 and lactic acid production No - Quentin Bet 09/27/2018 10:37:25 pm Gabby DeBartolomeo 09/27/2018 10:37:25 pm
Veilleux, B. G. (1979). An Analysis of the Predatory Interaction Between Paramecium and Didinium. Journal of Animal Ecology, 48(3), 787-803. predation Didinium nasutum Paramecium aurelia 60 x 15 mm Petri dishes containing 6 ml of culture medium, at 27 degrees C; liquid planktonic continuous aerobic aquatic environments, stillwater engineered Paramecium aurelia, syngen 4, stock 515, mating type VII visualization to determine densities at different Cerophyl concentrations cytosome engulfs prey; stable, non-oscillatory coexistence between the species is possible only at extremely low Cerophyl concentrations where the Didinium population is inefficeint; the efficiency of Didinium as a predator is directly related to nutritio No - Quentin Bet 09/27/2018 10:37:25 pm Kelsey Hyland 09/27/2018 10:37:25 pm
Coaggregation of Porphyromonas gingivalis and Fusobacterium nucleatum PK 1594 is mediated by capsular polysaccharide and lipopolysaccharide. commensalism coaggregation Porphyromonas gingivalis Fusobacterium nucleatum both species grown in Wilkins–Chalgren anaerobe broth under anaerobic conditions liquid, well-mixed planktonic biofilm batch culture both species are anaerobic human oral cavity natural radioactive labeling to determine cell density ; stastical analysis for differences using ANOVA followed by Scheffe multiple-comparison test capsular polysaccharide (CPS) and lipopolysaccharide (LPS) receptors on P. gingivalis bind to proteins on the surface of F. nucleatum No Gabby DeBartolomeo 09/27/2018 10:37:25 pm Isabel Brandenburger 09/27/2018 10:37:25 pm
Rypien, K. L., Ward, J. R., & Azam, F. (2010). Antagonistic interactions among coral-associated bacteria. Environmental Microbiology, 12(1), 28-39. antagonism 67 bacterial isolates (including two coral pathogens Vibrio shiloi and V. coralliilyticus) most common genera of the 67 bacterial isolates: Vibrionales & Alteromonadales bacteria isolated from coral sample and streaked on marine agar, stored and grown in marine broth ; bacteria from the scleractinian coral Montastrea annularis at two temperatures solid & liquid, well-mixed biofilm batch aerobic?; I think aerobic also microbial isolates obtained from three M. annularis coral colonies in the Florida Keys, USA natural buckholder diffusion assays imaged with a transilluminator, colony diameter and halo diamter measured with digital imaging software (antagonism was considered to occur when the diameter of the zone of inhibition was at least 1 mm greater than the diameter metabolic, bacteria induce or enhance antibiotic production, more research needed on the bacterial mechanisms of nutrient uptake, predation, and growth rates as antagonistic mechanisms...70% of tested bacteria demonstrated antibacterial activity at 25°C w no this evidence suggests a potential mechanism for the dramatic community shifts observed with warming temperatures coral-associated bacterial community does not appear to be dominated by a few strongly antagonistic bacteria, but rather coexistence occurs Kelsey Hyland 09/27/2018 10:37:25 pm Ryann Gutierrez; Kelsey Hyland 09/27/2018 10:37:25 pm
Harris, R. N. et al. (2009). Skin microbes on frogs prevent morbidity and mortality caused by lethal skin fungus. International Society for Microbial Ecology, 3, 818-824. amensalism, antibiosis antifungal bacteria: Janthinobacterium lividum chytrid fungus, Batrachochytrium dendrobatidison, on Rana muscosa frogs R. Muscosa frogs were innoculated with J. lividum and randomized to either a control group or an experimental group that was exposed to Bd zoospores spatial, in vivo sample on frogs skin biofilm batch aerobic R. muscosa frogs obtained from a labrotory colony from field collected eggs at University of California, Berkley, J. lividum obtained from skin of salamander, Hemidactylium scutatum, Bd Strain JEL was islolated from infected R. muscosa; high elevation pon natural frog skin swabbed with rayon swabs to detect Bd and J. lividum abundance, PCR used to test for prescence/abscence profile, violacein on skin collected after frogs were killed, repeated-measures ANOVA used to test for differences in the number of zoospores metabolic, morbidity and mortality caused by Bd was prevented by bioaugmentation of frog skins with J. lividum, survival of frogs was strongly associated with the prescence of violacein (an anti-Bd metabolite produced by J. lividum), five of six frogs in no frogs in the Bd treatment did not grow and lost some weight on average, frogs in the bacteria and bacteria+Bd treatment had no detectable zoospores equivalents on their skins from the first day of the sample (day 19) until the last day (day 139) Kelsey Hyland 09/27/2018 10:37:25 pm Ryann Gutierrez; Kelsey Hyland 09/27/2018 10:37:25 pm
Kapongo J. P., Shipp, L., Kevan P., & Sutton J. C. (2008). Co-vectoring of Beauveria bassiana and Clonostachys rosea by bumble bees (Bombus impatiens) for control of insect pests and suppression of grey mold in greenhouse tomato and sweet pepper. Biologic antagonistic (competition shown in other studies, exact competition/antagonistic mechanism not analyzed in this study) Clonosyachys rosea grey mold (Botrytis cinerea) in vitro in experimental and control greenhouses spatial, fixed samples collected from plants in greenhouses biofilm batch aerobic greenhouse tomatos and sweet peppers natural sweet peppers, tomatos, and bee colonies; engineered commerical formula of C. rosea used for the suppression of grey mold was innoculated on bee colonies in wooden inoculum dispensers at the exit and entry opening of hives; sweet peppers and tomat C. rosea inoculum left in dispenser was dried and weighed to determine the amount of inoculum that bumble bees delivered; plant leaves collected on petri dishes and cut using a dissecting microscope to determine incidence and percentage area of tissue pie metabolic, previous studies show C. rosea antagonizes B. cinerea through nurtient competition in wounded tissue, hyperparasitism, and competitive colonization of senescing and dead tissues, in this study grey mold incidence was significantly lower in plan no Kelsey Hyland 09/27/2018 10:37:25 pm Isabel Brandenburger; Kelsey Hyland 09/27/2018 10:37:25 pm
Interaction between fish spoilage bacteria Pseudomonas sp. and Shewanella putrefaciens in fish extracts and on fish tissue; Journal of Applied Microbiology Volume 80 Issue 6; L. Gram and J. Melchiorsen; Wiley Online library competition/antagonistic 5 Pseudomonas sp. isolates Shewanella putrefaciens fish-extract agar diffusion assay; 5 Pseudomona isolates identified by API NE system, belonged to fluorescens/ putida group; fish extract prepared from caught cod cut into pieces, boiled and filtered solid, well-mixed biofilm batch aerobic spoiled fish natural plating; siderophore production assayed on CAS agar and on fish extract FE agar ;interactions in fish extract agar on heat sterilized FE organism added to molten agar and poured into eptri dishes; wells punch into each plate and cultured organism added; metabolic, Pseudomonas strains product iron chelators that inhibit growth of S. putrefaciens; most inhibitory Pseudomonas were strongest siderophore producers No supernatant fluids from siderphore negative Pseudomonas isolates did not inhibit the growth of S. putrefaciens; when Pseudomonas lowered cell level of S. putrefaciens when strains were gorwn on fish muscle tissue Gabby DeBartolomeo 09/27/2018 10:37:25 pm Ryann Gutierrez 09/27/2018 10:37:25 pm
Cuervo-Parra, J.A., Ramírez-Suero, M., Sánchez-López, V., Ramírez-Lepe, M. (2011). Antagonistic effect of Trichoderma harzianum VSL291 on phytopathogenic fungi isolated from cocoa (Theobroma cacao L.) fruits. African Journal of Biotechnology, vol. 10(52), prey-predation Trichoderma harzianum strain VSL291 Moniliophthora roreri in vitro on potato dextrose agar (PDA) medium solid, spatial not specified batch T. harzianum is a facultative anaerobe, M. roreri is aerobic, grown in aerobic conditions T. harzianum lives in the soil, M. roreri lives on cocoa fruits natural interactions observed via plating, as well as light microscopy and scanning electron microscopy; confrontation experiments were analyzed using the biocontrol index and an imaging software to measure area of the colonies T. harzianum has high proteolytic enzyme activity which inhibits M. roreri growth No Peter Brand 09/27/2018 10:37:25 pm Connor Monahan, Peter Brand 09/27/2018 10:37:25 pm
Nutzmann, H., Reyes-Dominguez, Y., Scherlach, K., Schroeckh, V., Horn, F., Gacek, A.,... Brakhage, A.A. (2011). Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc of th commensalism Aspergillus nidulans Streptomyces rapamycinicus A. nidulans was incubated in Aspergillus minimal medium (AMM) both with and without S. rapamycinicus present solid, spatial not specified continuous aerobic A. nidulans and S. rapamycinicus live in the soil natural interactions observed via plating, as well as electron microscopy metabolic, S. rapamycinicus activates silent gene clusters such as PKS in A. nidulans which induces activation of biosynthesis of specific secondary metabolites No Peter Brand 09/27/2018 10:37:25 pm Connor Monahan, Peter Brand 09/27/2018 10:37:25 pm
Chamoun, R., Aliferis, K.A., Jabaji, S. (2015). Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans. Front. Microbiol., vol. 6, pp. 1-11. DOI: 10.3389/fmicb.2015.00353 competition (mycoparasitism) Stachybotrys elegans conidia Rhizoctonia solani AG-3 in vitro on potato dextrose agar (PDA) medium and minimal synthetic medium (MSMA) solid, spatial not specified batch aerobic S. elegans can live on R. solani hyphae, R. solani is a soil-borne pathogen that lives on plants natural interactions observed via plating, as well as optical microscopy metabolic, S. elegans conidia disrupts R. solani metabolism and suppresses biosynthesis of R. solani defense mechanisms such as antimicrobial metabolites No Peter Brand 09/27/2018 10:37:25 pm Connor Monahan, Peter Brand 09/27/2018 10:37:25 pm
Microbial Interactions and differention protein expression in Staphylococcus aureus -Candid albicans dual species biofilms; Brian M. Peters Mary Ann Jabra-Rizk Mark A. Scheper Jeff G. Leid John William Costerton Mark E. Shirtliff; Pathogens and Diseas mutualism?? Staphylococcus aureus Candida albicans S. aureus obtained from a patient with a biofilm mediated infection at the University of Texas Medical Branch; C. albicans lab strain SC5314 used for all experiments: S. aureus strain Seattle 1945 used and C. albicans straun CAF2-1. Experiment done in trials in both solid and liquid media done biofilm; in vitro biofilms batch aerobic S.aureus naturally found in the nose, respiratory tract, and skin of animals; C. albicans a fungal species commonly colonizing human mucosal surfaces natural strains were cultured on plates; determined nature and spacial releationship of interactions with Confocal scanner laser microscopy; characterized proteomic changes of polymicrobial culture of biofilm using 2 dimensional differential in gel electrophores S. aureus and C.albicans have hyphal associations; hyphae can penetrate through epithelial layers; preferential association to invasive hyphal elements of C. albicans. It was found that some genes are upregulated when the two microbes grow together in a yes; actual experimental images microbial association within a polymicorbial biofilm; both are significant human pathogens and seem to up regulate virulence factors of eachother when working together; S. aureus binds well to hyphal elements of C. albicans Ryann Gutierrez 09/27/2018 10:37:25 pm Lauren Bynum, Ryann Gutierrez 09/27/2018 10:37:25 pm
Peterson, S.B., Dunn, A.K., Klimowicz, A.K., Handelsman, J. (2006) Peptidoglycan from Bacillus cereus Mediates Commensalism with Rhizosphere Bacteria from the Cytophaga-Flavobacterium Group. Applied and Environmental Microbiology, vol. 72, pp. 5421-5427. commensalism Bacillus cereus Cytophaga-Flavobacterium (CF) group of the Bacteroidetes phylum strains grown in liquid culture tryptic soy broth, propogated on tryptic soy agar solid (propogation phase); well-mixed biofilm batch aerobic rhizosphere (area beneath the soil among plant roots) natural plating, colonies were purified by repeated streaking peptidoglycan produced by B. cereus stimulates the growth of CF bacteria; CF bacteria releases enzymes that break down the extracellular peptidoglycans for use by the CF bacteria as a source of carbon and energy Yes Gabby DeBartolomeo 09/27/2018 10:37:25 pm Peter Brand 09/27/2018 10:37:25 pm
Diaz, Patricia I., Linda D. Strausbaugh, and Anna Dongari-Bagtzoglou. Fungal-Bacterial Interactions and Their Relevance to Oral Health: Linking the Clinic and the Bench. Frontiers in Cellular and Infection Microbiology 4 (2014): 101. PMC. Web. 20 Apr. 2 commensalism, possibly mutualism Candida albicans Staphococcus Streptococcus oralis, part of the Mitis group streptococci (MGS) in vitro organotypic mucosal model and oral polymicrobial infection mouse model; salivary flow accounted for solid; spatial biofilm batch aerobic human oral microbiota natural co-occurrence and the effect on the surrounding infection unknown; perhaps extracellular polysaccharides, possibly metabolic; interaction enabled via specific adhesin-receptor mediated binding to form biofilms no 16S rRNA sequencing and internal transcribed spacer (ITS) profiles were also used to characterize the fungi present in the oral samples Isabel Brandenburger 09/27/2018 10:37:25 pm Peter Brand 09/27/2018 10:37:25 pm
Wei, Yan, Paolo Ocampo, and Bruce R. Levin. An Experimental Study of the Population and Evolutionary Dynamics of Vibrio Cholerae O1 and the Bacteriophage JSF4. Proceedings of the Royal Society B: Biological Sciences 277.1698 (2010): 3247-3254. PMC. Web. predation Vibrio cholerae N16961 JSF4 bacteriophage V. cholerae were grown in LB broth or medium of 5% LB and 95% tap water; cocultured in chemostats with 5% LB and 95% tap water; V. cholerae also cultured on Daphnia; all cutures at 30 deg. Celsius solid and liquid, well mixed bioflim, not specified continuous aerobic on the exoskeleton of copepods natural plating and dilution predation of V. cholerae by bacteriophage no Isabel Brandenburger 09/27/2018 10:37:25 pm Peter Brand 09/27/2018 10:37:25 pm
K.M. Old, S. Chakraborty, R. Gibbs, Fine structure of a new mycophagous amoeba and its feeding on Cochliobolus sativus, Soil Biology and Biochemistry, Volume 17, Issue 5,1985,Pages 645-655, predation unidentified mycophagous soil amoeba Cochliobolus sativus embedded in a 2% distilled water agar solid; spatial biofilm batch aerobic sandy loam wheatfield soil from the Eyre Peninsula in South Australia; and red basaltic loam soil from Burnie, NW Tasmania natural observed feeding through light microscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) predation of C. sativus by amoeba; the amoeba digests spore walls within food vacuoles by general erosion of the outer melanized layer followed by lysis of the protoplast no the irregular invaginations of the cell membrane may represent an increase in the surface area for passage of lytic enzymes from the amoebal protoplast to the spore wall Isabel Brandenburger 09/27/2018 10:37:25 pm Kelsey Hyland 09/27/2018 10:37:25 pm
Hennessy, Rosanna C. et al. “Transcriptomic Profiling of Microbe–microbe Interactions Reveals the Specific Response of the Biocontrol Strain P. Fluorescens In5 to the Phytopathogen Rhizoctonia Solani.” BMC Research Notes 10 (2017): 376. PMC. Web. 20 Apr. antagonism P. Fluorescens In5 (bacteria) R. Solani (fungus) Nunc™ OmniTray™ sterile plats prepared with 35mL of fifth strenght potato dextrose and R. Solani plugs placed in the center. P. Fluorescens In5 growm in 10ml of Luria-Bertani Brother overnight and streaked 3 cm away from fungal plugs. solid; spatial biofilm batch culture not specified (likely aerobic) aerobic P. Fluorescens found in soil in southern greenland. R. Solani is a common phytopathogen found on plants. natural Plating P. Fluoresens and R. Solani and observing zones of inhibition and RNA isolation and sequencing. P. Fluoresens antagonizes the phytopathogen R. Solani through the unpregulation of genes involved in the production of secondary metabolites and genes involved in detoxification. No Raw data available John Botzler 09/27/2018 10:37:25 pm Margaret DuChene, John Botzler 09/27/2018 10:37:25 pm
Mukherjee, Pranab K. et al. “Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi.” Ed. Deborah A. Hogan. PLoS Pathogens 10.3 (2014): e1003996. PMC. Web. 20 Apr. 2018. antagonism, competition Pichia (bacteria) Candida albicans (fungus) C. albicans maintained on Sabouraud dextrose agar (SDA plates). Pichia strain obtained from the OHARA Repository at Case and the culture collection of the Center for Medical Mycology. liquid, mixed at various ratios (mixed and monocultures), in vivo and in vitro, biofilm and planktonic continuous culture not specified (likely aerobic) oral microbiota of HIV infected patients natural Microbiome analysis used to identify bacteria and fungi present. Nutrient competition tested through mixing of Pichia and C. albicans at various ratios to observe nutrient depletion. Inhibition of C. albicans tested via germination and adhesion assay of Pichia antagonizes C. albicans through secratory proteins. Nutrient competition between Pichia and C. albicans played a role in the inibition of C. Albicans as well. No Raw data available John Botzler 09/27/2018 10:37:25 pm Margaret DuChene, John Botzler 09/27/2018 10:37:25 pm
Sen, Ruchira et al. Generalized Antifungal Activity and 454-Screening of Pseudonocardia and Amycolatopsis Bacteria in Nests of Fungus-Growing Ants. Proceedings of the National Academy of Sciences of the United States of America 106.42 (2009): 1780-1781 antagonism Pseudonocardia (fungus) Escovopsis isolated from 6 attine ant species. Pseudonocardia plated and isolated from Chitin medium. solid, spatial Biofilm batch culture aerobic fungal-growing (attine) ants engineered in laboratory, isolated from lab colonies Plating on Chitin medium plates and microscopic investigation. Identification via 16s RNA sequencing. Escovopsis is inhibited by the secretions of Pseudonocardia nonspecifically. Escovopsis also shown to be easily inhibited as it is inhibited by common yeasts which are not known to be strongly antibiotic. No Raw data available The non-specific model of inhibition contrasts the previously accepted model of a co-evolutionary arms race between Escovopsis and Pseudonocardia. John Botzler Margaret DuChene, John Botzler 09/27/2018 10:37:25 pm
Tan KH, Seers CA, Dashper SG, et al. Porphyromonas gingivalis and Treponema denticola Exhibit Metabolic Symbioses. Schneider DS, ed. PLoS Pathogens. 2014;10(3):e1003955. doi:10.1371/journal.ppat.1003955. Symbiosis Porphyromonas gingivalis (strain W50) Treponema denticola (strain ATCC 35405) Strains retrieved from the Oral Health Cooperative Research Centre at the University of Melbourne; strains were grown in oral bacterial growth medium (OBGM) in a Bioflo 110 Modulator Benchtop Fermentor Liquid, Well-mixed Planktonic Continuous Anaerobic Human mouth; subgingival plaque Naturally occurs in human mouth; these particular strains are laboratory stocks Population growth was assessed using both optical density and quantitative real-time PCR; DNA microarray analysis was used to screen for differential gene expression; glycine concentrations were assessed using both GC mass-spectrometry and NMR analysis of C-13 labeled glycine; P. gingivalis thiamine pyrophosphate production was evaluated by comparing growth in the experimental co-culture with growth in a co-culture of P. gingivalis and E. coli strain JW3957-1, a thiamine pyrophosphate auxotroph. P. gingivalis likely upregulates thiamine pyrophosphate biosynthesis in the presence of T. denticola (a thiamine pyrophosphate auxotroph). Other genes observed to have been up- or down-regulated: amino acid transport and metabolism in T. denticola and coenzyme transport and metabolism in P. gingivalis. P. gingivalis also up-regulates free glycine production in the presence of T. denticola, while T. denticola up-regulates glycine catabolic pathways in the presence of P. gingivalis and exhibits incresed growth. Yes; see "Supporting Information" Also, "the presence of T. denticola helps P. gingivalis reduce energy consuming processes which may explain the increase in cell biomass of P. gingivalis grown in the presence of T. denticola". Overall, the populations of P. gingivalis and T. denticola in co-culture were observed to increase by 54% and 30%, respectively, suggesting that the two species respond metabolically to each other in a way that helps explain the virulence of co-infections in vivo. Kyle Wiant Salvador Norton de Matos
Reece E, Doyle S, Greally P, Renwick J, McClean S. Aspergillus fumigatus Inhibits Pseudomonas aeruginosa in Co-culture: Implications of a Mutually Antagonistic Relationship on Virulence and Inflammation in the CF Airway. Frontiers in Microbiology. 2018;9:1205. doi:10.3389/fmicb.2018.01205. Mutual Inhibition Aspergillus fumigatus Pseudomonas aeruginosa Strains were co-cultured in CFBE41o- bronchial epithelial cells, as well as Galleria mellonella larvae, and on Malt Extract agar (MEA) plates In vivo in epithelial cells/larvae as well as solid/spatial on MEA plates Biofilm Continuous Aerobic Human airway, in cystic fibrosis patients Natural Population sizes of both species were assessed using both crystal violet biofilm analysis and species-specific qPCR A. fumigatus produces gliotoxin at 48 and 72 hours which inhibits P. aeruginosa and biofilm formation; previous studies cited in article have repeatedly shown that P. aeruginosa inhibits A. fumigatus through secretion of pyocyanin and 1-hydroxy-phenazine, two known antifungal agents. No This is the first study in which A. fumigatus has been shown to inhibit P. aeruginosa; previously, it was only known that P. aeruginosa inhibits A. fumigatus, and not vice versa. Kyle Wiant Salvador Norton de Matos
Kerr JR, Taylor GW, Rutman A, Hoiby N, Cole PJ, Wilson R. Pseudomonas aeruginosa pyocyanin and 1-hydroxyphenazine inhibit fungal growth. Journal of Clinical Pathology. 1999;52(5):385-387. Amensalism Pseudomonas aeruginosa Aspergillus fumigatus Responses to antifungal compounds were assessed using a well-plate assay on BHI agar flooded with a suspension of A. fumigatus Solid/spatial Biofilm Batch Aerobic Human respiratory tract Engineered; although these species are known to interact in vivo A well-plate assay on BHI agar flooded with liquid suspensions of indicator strains (in this case, A. fumigatus) was used to assess the degree of inhibition: after the plate had dried, liquid samples of the identified extracts were added to the plate, and inhibition was measured by evaluating the difference between the diameter of inhibition and the original diameter of the well. Pyocyanin (a known antifungal and antibiotic pigment) produced by P. aeruginosa appears to inhibit A. fumigatus growth No Kyle Wiant Salvador Norton de Matos
Kerr JR, Taylor GW, Rutman A, Hoiby N, Cole PJ, Wilson R. Pseudomonas aeruginosa pyocyanin and 1-hydroxyphenazine inhibit fungal growth. Journal of Clinical Pathology. 1999;52(5):385-387. Amensalism Pseudomonas aeruginosa Candida albicans Responses to antifungal products were assessed using a well-plate assay on BHI agar flooded with a suspension of C. albicans Solid/spatial Biofilm Batch Aerobic Human respiratory tract Engineered; although these species are known to interact in vivo A well-plate assay on BHI agar flooded with liquid suspensions of indicator strains (in this case, C. albicans) was used to assess the degree of inhibition: after the plate had dried, liquid samples of the identified extracts were added to the plate, and inhibition was measured by evaluating the difference between the diameter of inhibition and the original diameter of the well. Pyocyanin produced by P. aeruginosa seems to have some role in disrupting the yeast-mycelium transition in C. albicans, possibly by reducing cAMP, the lack of which impairs hyphae formation No Kyle Wiant Salvador Norton de Matos
Costello A, Reen F, O'Gara F, Callaghan M, McClean S. nhibition of co-colonizing cystic fibrosis-associated pathogens by Pseudomonas aeruginosa and Burkholderia multivorans. Microbiology 160(7):1474-1487 B. multivorans Pseudomonas aeroginosa
Lima, B.P., Hu, L.I., Vreeman, G.W. et al. The Oral Bacterium Fusobacterium nucleatum Binds Staphylococcus aureus and Alters Expression of the Staphylococcal Accessory Regulator sarA. Microb Ecol (2018). Mutualism Staphylococcus aureus [SH1000 lab strain] Fusobacterium nucleatum [ATCC 23726] Coculture of strains was grown in 50% SHI medium supplemented with 25% saliva, over 24 hours Liquid Biofilm Batch Anaerobic Human oral cavity Natural Coaggregation of S. aureus and other oral strains was first assessed visually (by amount of biofilm/aggregate produced). Crystal-violet-retention assay was then used to assess relative biofilm production in monocultures/coculture in liquid media. F. nucleatum surface protein RadD (used to bind with a number of oral species) allows S. aureus to bind and consequently increase biofilm formation compared to monoculture. F. nucleatum acts as an "anchoring point" for S. aureus and helps it integrate into the oral microbiome. Additionally, this interaction appears to upregulate S. aureus regulator sarA, which has been implicated in "pathogenicity, biofilm formation, and susceptibility to antibiotic treatment". No S. aureus was also grown in coculture with a previously-defined multispecies community, representative of dental plaque, in SHI media for 6 days. qPCR indicated that S. aureus was able to integrate into this complex community; see Fig. 5. Kyle Wiant
van Leeuwen PT, van der Peet JM, Bikker FJ, Hoogenkamp MA, Oliveira Paiva AM, Kostidis S, Mayboroda OA, Smits WK, Krom BP. 2016. Interspecies interactions between Clostridium difficile and Candida albicans. mSphere 1(6):e00187-16. doi:10.1128/mSphere.00187-16. commensalism; inhibition Clostridium difficile Candida albicans C. diff maintained on BHI containing 1.5% [wt/vol] Bacto agar at 37C under anaerobic conditions (10% H2, 10% CO2 in N2). C. albicans maintained on yeast-peptone-dextrose (YPD) agar (1% [wt/vol] Bacto yeast extract, 2% [wt/vol] Bacto peptone, 2% [wt/vol] dextrose [Merck], 1.5% [wt/vol] Bacto agar) at 30C under aerobic conditions. Cocoluture incubated for 30 h under anaerobic conditions at 37C in test tubes. liquid; spatial planktonic/biofilm batch aerobic; anaerobic human gut engineered using lab strains Growth evaluated using OD600 in monoculture and coculture to determine that Candida albicans enables aerobic growth of the obligate anaerobe Clostridium difficile. Adhesion assay used to determine that C. difficile does not adhere to C. albicans hyphae. Growth of C. difficile in presence of oxygen hypothesized to be mediated by C. albicans-produced antioxidants or oxygen takeup by the fungus for cellular respiration, thereby decreasing oxygen concentrations. C. albicans morphology shift and biofilm inhibition is due to the presence of signals secreted by C. difficile during stationary phase, specifically p-cresol. https://msphere.asm.org/content/1/6/e00187-16/figures-only Aidan Pavao Sarah Ryan
Leclercq-Perlat, M. N., et al. Behavior of Brevibacterium Linens and Debaryomyces Hansenii as Ripening Flora in Controlled Production of Soft Smear Cheese from Reconstituted Milk: Protein Degradation. Journal of Dairy Science, vol. 83, no. 8, 2000, pp. 1674-83, doi:https://doi.org/10.3168/jds.S0022-0302(00)75036-3. Mutualism Debaryomyces hansenii Brevibacterium linens One strain of D. hansenii 304 (L.G.M.P.A. collection, Grignon) and one strain of B. linens ATCC 9175, isolated from a cheese surface, and lactic bacteria cultures (Lactococcus lactis ssp. lactis CNRZ 1128 and its non-protease variant 1130) were used as rippening starters. Smear soft cheeses (30 cheeses per production run, each weighing about 350 g) were manufactured in a sterile environment (20). The cheeses were aseptically transferred to a ripening chamber previously sterilized with peracetic acid (Soproper, Seppic, France) and maintained for 24 h at 14C and 80% RH spatial not specified batch available cheese natural Measured DM, pH, lactose and lactate concentrations for each part of the cheese. Determined the content of nitrogen compounds as well as the ASN and NPN filtrates with the Kjeldahl method. The ratios of ASN/TN and NPN/TN were used as cheese-ripening indicators. Total nitrogen (TN) was measured according to the IDF standard. Acid-soluble nitrogen (ASN) and NPN were also determined. It was shown that the inner cheese pH and populations of D. hansenii and B. linens have an effect on proteolysis. Viable cell counts of D. hansenii and B. linens were correlated with the environmental conditions and with proteolytic products. The viable B. linens cell population (given in the accompanying paper; 20) was positively correlated with ASN (Table 2). Famelard et al. (10) elucidated the role of peptides and amino acids as growth factors for B. linens in an oxygenated liquid medium. D. hansenii oxidizes lactic acid, raising the pH to a level suitable to the growth of B. linens. It produces intrapeptidase activities. B. linens contributes to ripening by the production of flavor compounds and by its proteolytic activities. no Maya Coley Sarah Ryan
Dourado M.N., Santos D.S., Nunes L.R., Costa de Oliveira R.L., de Oliveira M.V., Araujo W.L. Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6. J Basic Microbiol. 2015;55:1357-1366. [PubMed] parasitism (phytopathogen-endophyte) X. fastidiosa strain 9a5c M. mesophilicum strain SR1.6/6 X. fastidiosa cells were grown, separately, in 300 ml of PW medium, and M. mesophilicum SR1.6/6 cells were grown in 300 ml of SPW medium; both cultures were incubated for 72 h at 28C (150 rpm). On the 3rd day, 100 mL from each individual cell suspension (108 CFU ml?1) were mixed together (totaling 200 ml). The remains from each original culture (200 ml) were kept in separate flasks without interaction, to serve as controls. Co-cultivation experiment planktonic cells Batch culture available Citrus plants (X. Fastidiosa is the causal agent of citrus variegated chlorosis) natural evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. Constructed X. fastidiosa microarrays X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium. X. fastidiosa genes are regulated by the presence of the endophytic bacteria M. mesophilicum. no Maya Coley Sarah Ryan
Chamoun R., Aliferis K.A., Jabaji S. Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans. Front Microbiol. 2015;6:353. [PubMed] Mycoparasitism Stachybotrys elegans Rhizoctonia solani Starter cultures of the mycoparasite Stachybotrys elegans (Pidoplichko) W. Gams (ATCC 18825) and the pathogen Rhizoctonia solani AG-3 (ATCC 10183) were revived from pre-colonized oat kernels on 1% potato dextrose and incubated at 24C for 7 and 5 days, respectively Dual-culturing of S. elegans and R. solani was conducted in 9 cm Petri plates containing 20 mL of minimal synthetic medium. Agar plugs (8 mm) of a 5-day old R. solani culture were grown on MSMA for 48 h and then sprayed with 100 uL of a suspension of S. elegans conidia. Also emplowed positive and negative control plates. Dual culturing as well as spraying suspension of S. elegans (minal media plates) Planktonic Batch culture available Fungal disease on crops engineered direct-infusion mass spectrometry (DIMS) metabolomics analysis using an LTQ Orbitrap analyzer in order to detect changes in the profiles of induced secondary metabolites of both partners during this mycoparasitic interaction 4 and 5 days following its establishment The majority of the antimicrobial R. solani-derived metabolites were down-regulated in dual-cultures possibly due to the direct effect of the mycoparasite on host's metabolism or because they were produced in trace amounts. Alternatively, S. elegans mycotoxins known as trichothecenes were up-regulated during mycoparasitism. no Maya Coley Jessica Urbanczyk
Partida-Martinez L.P., Hertweck C. Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature. 2005;437:884-888 plant-pathogen-symbiont model(between bacteria and fungus in a plant) Rhizopus sp. F-1360 (ATCC 20577) Burkholderia R. microsporus van Tieghem var. chinensis (ATCC 62417) Rhizopusstrains were grown on potato glucose agar medium at 30C. Liquid fermentation was carried with 100 ml seed medium (1% corn starch, 0.5% glycerol, 1% gluten meal, 1% dried yeast, 1% corn steep liquor and 1% CaCO3, pH 6.5) at 30C with agitation between 40 and 80 r.p.m R. microsporus, cultivated in the presence of ciprofloxacin (20-40 ug ml-1, Bayer AG). onto 5-day old R. solani culture. Strains were cultured on solid media and then fermentation was carried out in liquid media. Unclear Constantly cultivated, available Rice seedlings, soil natural Isolated bacterial symbionts, used laser microscopy, and HPLC-MS analyses. Amplified the KS gene from fungal metagenomic DNA and then amplified 16s rDNA. The 16s rDNA was sequenced. chemical signals in the fungal-bacterial association trigger and/or maintain rhizoxin biosynthesis in the state of symbiosis. fungus hosts a bacterial population for the production of the causative agent of rice seedling blight. Rhizoxin, which inhibits mitosis in rice plant cells, efficiently weakens or even kills the plant, and both host and symbiont benefit from nutrients from decaying plant material no Maya Coley Jessica Urbanczyk
Nogueira, M. F., Pereira, L., Jenull, S., Kuchler, K., & Lion, T. (2019). Klebsiella pneumoniae prevents spore germination and hyphal development of Aspergillus species. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36524-8 Antagonism Aspergillus fumigatus Klabsiella pnuemoniae (ATCC13883 and ATCC700603) For qualitative assessment of bacterial-fungal interaction, Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium at 37C. For co-culture experiments, fungi and bacteria were either mixed at time zero or K. pneumoniae strains were added after pre-germination of Aspergillus spores. solid media (Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium (Formedium, Norfolk, UK) at 37C. biofilm batch aerobic lungs and intestines natural The level of inhibition of fungal spore germination was assessed by qPCR at 24?h and imaged by confocal microscopy (to measure the biofilm thickness the Aspergillus spp). The results indicated that K. pneumoniae is able to prevent Aspergillus species spore generation and hyphal interaction and is dependent on direct interaction with metabolically active bacteria as evidened by the reversibility of this inhibition. In addition, molecular analysis of the interacion shows that the Aspergillus species will upregulate cell wall related genes and downregulate hyhal related genes when interacting with K. pneumoniae. The exact mechanism for these effects is not known with certainty. no Patrick Lima Jessica Urbanczyk
Mink, R. , Sommer, S. , Kolling, R. , Schmarr, H. and Scharfenberger?Schmeer, M. (2014), Diacetyl formation during vinification. Australian Journal of Grape and Wine Research, 20: 194-198. doi:10.1111/ajgw.12076 cooperation Oenococcus oeni Saccharomyces cerevisiae S. cervisiae is inoculated into grape juice, initial pH 3.2 and composition of glucose 94.3?g/L, fructose 89.9?g/L, L?malic acid 3.5?g/L, ethanol <0.5?g/L, tartaric acid 5.9?g/L, gluconic acid 0.1?g/L, nitrogen by ortho?phthalaldehyde 131?mg/L and NH4+ 70?mg/L and 24 hours later freeze dried O. oeni is added. Cell counting was done on solid MRS media treated with cycloheximide. liquid biofilm batch aerobic on the skin of fruit and in rotting fruit natural Gene expression analysis was done on the pyruvate pathway of O. oeni and PCR was taken of the O. oeni in the presence of S. cerevisiae and the products of fermentation were analyzed in the presence and absence of O. oeni to determine what the interaction effect is. S. cerevisiae in the presence of O. oeni increases diacetyl concentration during fermentation of wine, while decreasing citrate and L-malic acid No Claire McCann Jessica Urbanczyk
Bacterial interactions and Successions during plaque development, Kolenbrander et al., Periodontology 2000, Volume 42, 2006, 47-79 symbiosis Streptococcus gordonii Veillonella atypica Cells of both species were cutured together on agar plates containing starch as a carbohydate source, as well as in liquid context of flowcells. They were also cultured separately in dialysis bags, allowing exchange of medium but not cells. liquid in natural environment, but also culturable on solid media. Exists both as planktonic cells and in biofilms batch aerobic saliva of human mouth/dental plaque natural 1. Species on agar plates w/ starch together and as monocultures, only where seen together was strch hydrolzyed. 2. GFP was engineered to be under the control of promoter amyB, which increases strch hydrolysis. A plasmid containing PamyB-gfp was transformed into S. Gordonii, and cocultured with A. typica: only S. gordonii in juxtaposition with A.typica expressed GFP. 3. Species placed separately in dialysis bags, and GFP expression transformed S. gordonii was quantified in comparison to S. gordonii grown alone. Cell signaling. In a flowing environment, cells need cell to cell contact to complete signaling. In a closed environement, cell to cell contact is not neccessary. Interaction involves the production of lactic acid vis fermentation of carbohydrates by S. gordonii and fermentation of lactic acid by V. atypica no Joan Donahue Aidan Pavao
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Jeremy J. Minty, Marc E. Singer, Scott A. Scholz, Chang-Hoon Bae, Jung-Ho Ahn, Clifton E. Foster, James C. Liao, and Xiaoxia Nina Lin PNAS September 3, 2013 110 (36) 14592-14597; https://doi.org/10.1073/pnas.1218447110 mixed (cooperation and competition) Trichoderma reesei, fungus Escherichia coli, bacterium The T. reesei and E. coli were cultured in liquid TMM media at 30 degrees Celsius in a bioreactor. The E. coli cultures were treated wuth ampicillin, kanamycin, and isopropyl-?-D-thiogalactopyranoside. cultured in liquid media not specified in the source batch aerobic N/A-engineered interaction engineered Rate expressions were determined for the different metabolic products (including isobutanol, various carbohydrates, and protein content) of both the T. reesi and the E. coli and then these expressions were used to analyze the microbes present. Likewise, the growth was assessed using dry mass and total cell counts. Enzyme activity was also observed for endo/exoglucanase and ?-glucosidase. Metabolic interaction in which T. reesi releases cellulase and E. coli utilizes the products of the resulting hydrolysis without having to deal with the energy cost of producing and releasing the cellulase. Interaction demonstrates cooperator-cheater dynamic. There is also evidence of competition for saccharides. Yes https://www.pnas.org/content/pnas/suppl/2013/08/14/1218447110.DCSupplemental/sapp.pdf The production of isobutanol through this interaction is used as a proof of concept for other engineered biofuels as alternative energy sources. Further research is needed. Amanda Bourne Danielle Rinaldi
Effects of Bacteria on mycorrhizal development and growth of container grown Eucalyptus diversicolor F. Muell. seedlings symbiosis Laccaria fraterna (fungus) Bacillus sibtilis Fungi and bacterial were isolated from mycorrhiza. Fungi was grown on Palchleweski's medium at 22 degrees celcius and plugs were removed from the edges of colonies. Bacterial isolates were grown in Tryptic Soy Borth and resuspended in saline. Plugs were then inoculated with bacterial saline or TSB diluted with saline. Petri dishes were grown at 22 degrees, and after 6 days were irrigated with sterile glucose in saline. solid media biofilm batch aerobic sporocaps associated with Eucalytpus plants natural Fungal plugs inoculated with bacterial saline and TSB-saline were examined for growth after 14 days and measured under a stereoscope. Growth was analyzed using a T-test. unknown no Joan Donahue
A mycorrhiza helperbacterium enchances ectomycorrhizal and endomycorrhizal symbiosis of Australian Acacia species, R. Duponnois and C. Plenchette,Mycorrhiza (2003) 13:85-91 DOI 10.1007/s00572-002-0204-7 symbiosis Psuedomonas monteilii (bacteria) Pisolithus alba (fungus) Fungi was grown on solid agar plates in dark at 25 degrees C. Agar plugs were removed and incculated wtih bacteria. cultured on solid agar plates biofilm batch aerobic In association with acacai roots natural Fungal isolates were grown on agar plates for two weeks in the dark at 25 degrees C. Two agar plugs were removed and one was incolutated with bacteria. Fungal growth was assessed after 1 week with aid of stereoscope, and tested for significance. unknown no May be useful for improving growth of Acacai tree species Joan Donahue Ashley Bodnar
Zuroff, Trevor R et al. Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture Biotechnology for biofuels vol. 6,1 59. 29 Apr. 2013, doi:10.1186/1754-6834-6-59 symbiosis (obligate mutualism) Saccharomyces cerevisiae cdt-1 Clostridium phytofermentans S. cerevesiae and C. phytofermentans were grown a specified GS2 media. For the S. cerevesiae either cysteine, glutathione, or YPC was removed from the GS2. Varying concentrations of ?-Cellulose was also varied based on the culture(some had a starting source of carbon to see effects on growth). The C. phytofermentans came from cultures kept at -80 degrees Celsius. After the cultures were all prepared, they were incubated at 30 degrees Celsius in bioreactors. The entire experiment took place over 50 days. liquid cultures planktonic batch aerobic and anaerobic N/A engineered Optical Density was used to determine the ability of the cells to grow in the environment of the dissolved oxygen. Both monocultures of C. phytofermentan and bicultures between S. cerevesiae and the C. phytofermentan were observed. Based on the absorbance values, the C. phytofermentan monoculture experienced no growth, while the biculture resulted in rapid growth of both species. Some imaging was also included for analysis with the cultures with the extra source of carbon on the filter paper. Since the C. phytofermentan was only able to grow in the environment containing dissolved oxygen when the S. cerevesiae was present, it is assumed that the S. cerevisiae consumes the oxygen for its own growth, shielding the obligate anaerobe, C. phytofermentan. The C. phytofermentan then provides a soluble sugar source(?-cellulose) for the S. cerevesiae as it grows and converts it into ethanol internally. yes, seen in source link This research is important in developing engineered consortia to efficiently produce biofuels. Amanda Bourne Danielle Rinaldi
Zuroff, Trevor R et al. Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture Biotechnology for biofuels vol. 6,1 59. 29 Apr. 2013, doi:10.1186/1754-6834-6-59 symbiosis (obligate mutualism) Candida molischiana Clostridium phytofermentans The C. phytofermentans were grown in specified GS2 media. The yeast species, C. molischiana was grown in GS2 media not including cysteine, glutathione, or YPC. The C. phytofermentans came from cultures kept at -80 degrees Celsius and then were inoculated into the liquid media for the fermentations. All of the cultures were incubated 30 degrees Celsius until the desired growth concentrations had been reached. The growth was monitored for 50 days. liquid cultures planktonic batch aerobic and anaerobic N/A(natural microbiota consortia) engineered The amount of cell growth was used to determine the effectivity of the mutualistic relationship between the two species, C.molischiana and C. phtyofermentan. Cell growth was measured using optical densities. The amount of growth indicated the anaerobic C. phtyofermentan ability to survive in an environment containing oxygen, indicating a mutualist relationship with the C. molischiana. Some imaging was also included for analysis with the cultures with the extra source of carbon on the filter paper. The C. molischiana allows the C. phytofermentan to grow in the aerobic environment by consuming the oxygen, protecting the anaerobic C. phytofermentan from the oxygen. The C. molischiana produces a soluble carbon source for the C. molischiana, which in turn produces ethanol. The C. molischiana breaks down the carbon source for ethanol with ?-glucosidase. yes, seen in source link The production of ethanol is important for future developements in the microbe consortia-mediated production of biofuels. Amanda Bourne Katie Piccioli
Alsam, S. (2006). Escherichia coli interactions with Acanthamoeba: a symbiosis with environmental and clinical implications. Journal of Medical Microbiology, 55(6), 689-694. https://doi.org/10.1099/jmm.0.46497-0 Symbiosis Escherichia coli Acanthamoeba castellanii A. castellanii was grown in 24-well plates in PYG medium (5x10 5 amoebae ml ?1 per well) until confluent. The cells were washed once with PBS. Next, E. coli strains [2-10 6?c.f.u. per well (per 0.5?millilitre PBS)] were added, and the plates incubated for 1?h at room temperature. Liquid media Planktonic cells In situ Aerobic Soil and fresh water Natural E. coli association assays were performed with A. castellanii for both virulent and nonvirulent E. coli strains. The A. castellanii were exposed to the E. coli strains and following incubation, were lysed and associated bacteria were counted by plating on an agar nutrient plate. Invasion and intracellular survival assays were also performed, with A. castellanii cells lysed post incubation to count the number of intracellular bacteria present. E. coli association with A. castellanii through A. castellanii uptake of virulent E. coli. Proteins OmpA and LPS need to be present in E. coli for it to be associated with A. castellanii. OmpA is also crucial for E. coli survival inside the cell. Yes, available in source link OmpA and LPS are two extracellular proteins present on E. coli that are essential to invade and survive inside A. castellanii. The study was conducted to test the hypothesis that free living E. coli use A. castellani as a vector for neonatal meningitis. Salvador Norton de Matos Maya Coley
Axelsson-Olsson, D., Waldenstrom, J., Broman, T., Olsen, B., & Holmberg, M. (2005). Protozoan Acanthamoeba polyphaga as a Potential Reservoir for Campylobacter jejuni. Applied and Environmental Microbiology, 71(2), 987-992. https://doi.org/10.1128/aem.71.2.987-992.2005 Symbiosis Acanthamoeba polyphaga Campylobacter jejuni A. polyphaga trophozoites were grown for 48 hours in 12-well culture plates to in PYG broth to allow amoebae to attach to well surface. C. jejuni strains were isolated from a human patient and introduced of bacteria to the amoebae. Infection of amoeba were performed by adding 100 uL of bacteria in PYG solution to the plate wells. Cocultures were incubated aerobically at four different temperatures - 4, 10, 25, 30C. LIquid media Biofilm In situ Aerobic C. jejuni found in poultry products; A. polyphaga found in soil, dust air and water Natural Phase contrast microscopy was used to determine whether the C. jejuni cells had entered the amoebae. Images were taken at regular time intervals. Ten microliters of each sample was investigated at a magnification of 1,000 in a wet mount. Intracellular bacterial cells were viewed with in situ fluoresence hybridization. Additionally, each coculture was tested for culturability of the bacterial cells to examine the growth of C. jejuni colonies from ruptured amoeba. C. jejuni was observed to cluster at certain locations near the amoeba wall. After 1 hour, some C. jejuni were observed inside the amoeaba cells. Invading bacterial cells were seen highly motile within the amoeba, though restricted to amoebic vacuoles. C. jejuni that had infected the amoebas were able to survive and multiply within the cells. Yes, url link given in text, but link is broken. C. jejuni is highly sensitive to outside environments and it was hypothesized that A. polyphaga were being used as vectors for their transmission. Salvador Norton de Matos Maya Coley
Mengue, L., Ragnacq, M., Aucher, W., Portier, E., Hochard, Y., & Samba-Louaka, A. (2016). Legionella pneumophila prevents proliferation of its natural host Acanthamoeba castellanii. Scientific Reports, 6(1). https://doi.org/10.1038/srep36448 Antagonism Legionella pneumophila Acanthamoeba castellanii A. castellanii were seeded in 24-well pltes at 1x10^4 cells per well in Page's Amoeba Saline solution for 2 hours at 30C. Once cells adhered, bacteria that reached an OD600 of more than 2.3 were added to the amoeba at different multiplicity of infectin. Infection was synchronized by centrifugation. Cocultures were incbuated for 2 hours at 30 degrees C and cultured within the peptone-yeast-glucose medium and incubated at 30C. Solid media Biofilm In situ Aerobic Water and soil Natural A. castellanii were infected with L. pneumophila in a u-Slide 8 well IbiTreat microscopy chamber for two hours. Microscopy was conducted with confocal spinning disk microscope with mounted camera. A. castellanii proliferation was estimated by harvesting at different time points and counted in triplicate for each condition using plastic counting slides FastRead 102. L. pneumophila inhibited A. castellanii prolifferation with a functional Dot/Icm T4SS secretion system. L. pneumophila also induces modifications in shape, motility and cell division of A. castellanii. A. castellanii DNA replication was also inhibited by L. pneumophila. Yes L. pneumophila inhibits the proliferation of its natural host A. castellanii. Salvador Norton de Matos Maya Coley
Gibson, J., Sood, A., & Hogan, D. A. (2008). Pseudomonas aeruginosa-Candida albicans Interactions: Localization and Fungal Toxicity of a Phenazine Derivative. Applied and Environmental Microbiology, 75(2), 504-513. https://doi.org/10.1128/aem.01037-08 Antagonism Psuedomonas aeruginosa Candida albicans P. aeruginosa was innoclated onto preformed lawns of C. albicans onto the surface of the plate grown fungal culture. Solid media Fungal lawns and free-living bacteria In situ Aerobic Soil Natural Viability of fungal cells were determined microscopically using a hemocytometer. Methylene blue staining was also used to assess C. albicans survival. Metabolic interaction. P. aeruginosa and C. albicans were cocultured on solid media and produced a red pigmentation that was dependent on P. aeruginosa phenazine biosynthetic genes. P. aeruginosa prodced a precursor to pyocyanin (hypothesized to be 5-methyl-phenazinium-1-carboxylate), which was necessary for the formation of red pigmentation. This pigment accumulates heavily in fungal cells where it retained the ability to be reversibly oxidized and reduced. This resulted in decreased fungal viability. Yes This article proposes that intracellular targeting of some phenazines may contribute to its toxicity and could potential be useful in developing new antifungals. Salvador Norton de Matos Sarah Ryan
Kruse, S., Goris, T., Westermann, M., Adrian, L., & Diekert, G. (2018). Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07342-3 Syntrophy Sulfurospirillum multivorans Methanococcus voltae The coculture grown on a 15 mM lactate plate that included leucine, isoleucine, and casamino acids. The culture was cultivated under anaerobic conditions at 28C in a defined mineral medium without vitamin B12 (cyanocobalamin). Solid media Cells aggregated in extracellular polymeric substances Batch Anaerobic Sand Natural Electron microscopic analysis was used to determine the presence of cell aggregates. Since S. multivorans is not able to grow on lactate alone, the presence of these aggregates demonstrates the relationship between the two microbes. S. multivorans depends on M. voltae for the electron donor uptake (Hydrogen) in order to sustain a low hydrogen gas partial pressure, which therefore allows for hydrogen production to be thermodynamically favorable. No For Interaction mechanism put "S. multivorans depends on M. voltae for the electron donor uptake (Hydrogen) in order to sustain a low hydrogen gas partial pressure, which therefore allows for hydrogen production to be thermodynamically favorable." Also, for your citation put, "(Kruse, S., Goris, T., Westermann, M., Adrian, L., & Diekert, G. (2018). Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07342-3)". Listing the title of the article is not sufficient. Additionally, I believe the interaction occurs in nature and is therefore not engineered in this particular case. Also, it's "Syntrophy" not syntropy. Ryan Oleynik Patrick Lima
Bacteroides fragilis Prevents Clostridium difficile Infection in a Mouse Model by Restoring Gut Barrier and Microbiome Regulation Commensalism Bacteroides fragilis C. difficile C. difficile strain VPI 10463 was cultured anaerobically in sterile tubes containing 4 mL of TSB supplemented with 20% FBS at 37?C in an anaerobic glove box for 24 hours. The toxigenic spores from the C. dificile were administered to the model mice at a dose of 3 x 10^8 colony forming units (cfu) by oral gavage from Day 0 for 3 consecutive days. In vivo mouse model and in vitro Planktonic cells In situ Aerobic Gut Engineered The researchers monitored transepithelial electrical resistance (TEER) values for Caco-2 cells under C. dificile (control), exclusion (infected with B. fragilis for the first hour and C. difficile added for the second hour), competition (coinfected with C. dificile and B. fragilis), and substitution conditions (C. difficile were added for the first hour and B. fragilis added for the second hour). B. fragilis causes increased TEER values which prevent the colonization of C. dificile to Caco-2 cells (human epithelial colorectal adenocarcinoma cells). No This research lays the groundwork for further studies regarding the use of microbes in order to treat patients with C. dificile infection. This is important because non-antibiotic treatments are needed. Ryan Oleynik Patrick Lima
Adhesion of probiotic strains to the intestinal mucosa and interaction with pathogens Amensalism E. coli O157:H7 Bifidobacterium lactis DR10 Intestinal cell monolayer was used for some parts of the study and Caco-2 cells obtained from colon carcinoma were used as a model of the intestinal epithelial barrier for other parts of the study Fixed sample of cells from mouse in-vivo host; not specified whether the culture media was liquid or solid Not specified in situ Anaerobic Gut Natural In vitro and in vivo - growth of pathogenic bacteria (E. coli) in the presence of B. lactis. Otherwise unspecified. B. lactis adheres to mucosa in various segments of the gut and intestinal contents which prevents adherence of E. coli and thus its pathogenic effect No Danielle Rinaldi Katie Piccioli
Oral anaerobes cannot survive oxygen stress without interacting with facuItative/aerobic species as a microbial cornrn u n ity D.J. Bradshaw, P.D. Marsh, G.K. Watson and C. Allison Commensalism/mutualism (did not assess effect of F. nucleatus to N. subflava) Fusobacterium nucleatum ATCC 10953 Neisseria subflava 2 stage chemostat system, where stage 1 was a steady dilution rate and stage 2 was the "biofilm chemostat" vessel. Temperature was maintained at 37C and pH at 7.0 +/- 0.1. Each vessel was supplemented with 2.5g/l of porcine gastic mucin. Biofilms were induced using hydroxyapatite (HA) disks. Redox was monitored throughout the phases. Liquid cultures containing 3 other anaerobic microbes: Veillonella dispar ATCC 17745, Prevotella nigrescens T588, and Porphromonas gingivalis W50. Planktonic and biofilm (data did not support that biofilms aided anaerobe growth) Stage 1: continuous Stage 2: batch Aerobic Mouth Natural Serial dilution and plating on selective and non-selective media N. subflava consumes the oxygen that is otherwise toxic to F. nucleatum, allowing it to survive in an oxygenated environment despite its identity as an obligate anaerobe No These interactions were assessed within the context of a microbial community. The other anaerobic microbes present also demonstrated similar relationships with N. subflava. It has not been assessed whether these relationships would exist in different contexts. The mechanism for this interaction is not fully understood, and it is unknown whether the anaerobic microbes contribute something beneficial to N. subflava. Danielle Rinaldi Amanda Bourne
Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation Authors: Angela La, Patrick Perre, Behnam Taidi1 Mutualism Saccharomyces cerevisiae Chlorella vulgaris non-aerated photo-bioreactor (PBR) that contained a fermentation lock to prevent gases from being exchanged with the atmosphere. The temperature was maintained at 25C and the pH was controlled at 6.5 with automatic base KOH or acid H3PO4. Light was provided during inducbation. Liquid, Mixed culture Planktonic Batch Anaerobic S. cerevisiae-surface of fruit, however used in fermentation C. vulgaris-fresh water. Microbes have different habitats, growing together Engineered To monitor the proportion of populations, a flow cytometric method was used to determine the cell concentration of each population. Dissolved O2 and CO2 were continuously measured in-line to evaluate the in situ gas exchange between the two species and to proof the mutual symbiosis. Glucose and ethanol measurement, and dry weight are also used for analysis. S. cerevisiae produces CO2 which can then be used by C. vulgaris for photosynthesis. During photosynthesis, O2 is produced which can be used by S. cerevisiae. No This paper suggests that the symbiotic relationship discussed could result in potential savings for industries using fermentation technology. This is due to recovering the cost of the substrate that is normally lost as CO2, lowering the amount of gas supply needed and reducing environmental CO2 emissions. Ryan Oleynik Mingyun Wang
uan Liang, Andreas Klingl, Yen-Yu Lin, Emily Boul, Jane Thomas-Oates, Macarena Maran; A sub-compatible rhizobium strain reveals infection duality in Lotus, Journal of Experimental Botany, , erz057, https://doi.org/10.1093/jxb/erz057 Commensalism Rhizobium leguminosarum Norway Lotus burttii Bacteria inoculated to plants grown in sterile jars containing 300mL of sand:vermiculite mixture supplemented with 40mL FAB medium; Bacteria inoculated to plants grown on sterile filter paper (Whatman) on square petri platescontaining FAB medium Solid media, spatial Biofilm In situ, batch culture N/A Rhizosohere legumes of lotus species Natural Histological staining and fluorescence microscopy; Quantitative anlysis of images using Fiji v.2.0.0-rc-59/1.51j; Electron microscopy (Zeiss EM 912 transmission electron microscopy); Quantitative RT-PCR; Nod factor structure determination using Bruker 9.4 T solariX HR Fourier-transform ion cyclotron resonance instrument at CoEMS; conjugation; Stastical analysis using R-studio Lotus allows bacteria cells internalization through both trans-cellular infection threads and "peg"-like structures depending on the rhizobia strain encountered. Yes Experiments demonstrated that the internalization of rhizobia into plants is diverse, which fit the natural environment condition, where interactions of different strains are possible Mingyun Wang
Lawrence A. Klobutcher, Katerina Ragkousi, & Peter Setlow. (2006). The bacillus subtilis spore coat provides eat resistance during phagocytic predation by the protozoan tetrahymena thermophila. Proc. of the Nat. Acad. Sci. of the USA, 103(1), 165-170. doi:10.1073/pnas.0507121102 predation Bacillus Subtilis (all strains used were isogenic derivatives of strain PS832, a prototrophic derivative of strain 168) Tetrahymena thermophila (strain CU428.2) B. subtilis were selected for appropiate resistance to antibiotics including: kanamycin; chloramphenicol; tetracycline; spectinomycin; or lincomycin plus erythromycin. Spores of all strains were prepared at 37C on 2 SG medium agar plates without antibiotics, cleaned, and stored. T. thermophila was grown on SPPA medium containing penicillin, streptomycin sulfate, and amphotericin B at 30C. For spore ingestion experiments, T. thermophila cultures were initiated by adding 0.5 ml of a stock culture to 9.5 ml of fresh SPPA medium and culturing overnight. The cells were starved for 2-4 h at room temperature before use in spore ingestion experiments. solid media Planktonic batch culture Aerobic B. subtilis is naturally found in soil and vegetation. T. thermophila is a freshwater organism that inhabits streams, lakes, and ponds. Engineerd Tetrahymena cells were monitored by brightfield microscopy, and spores were examined by phase-contrast microscopy. Live Tetrahymena cells were photographed by using a Nikon Diaphot-TMD microscope. For measurements of phagosome size, cells were fixed in 2.5% formaldehyde before photography. Wild-type dormant spores of B. subtilis were efficiently ingested by T. thermophila but were neither digested nor killed. Spores with various coat defects were killed and digested, leaving only an outer shell termed a rind, and supporting the growth of Tetrahymena. A rind was also generated when coat-defective spores were treated with lysozyme alone. The sensitivity of spores with different coat defects to predation by T. thermophila correlated to the spores sensitivities to lysozyme. Spore killing by T. thermophila was done by the lytic enzymes within the protozoal phagosome, and not by initial spore germination followed by killing. Yes; table 1 and figures 2 and 3 These findings suggest that a major function of the coat of spores of B. subtilis is to protect spores against predation. The study also found that the indigestible rinds were generated even from spores in which cross-linking of coat proteins was greatly reduced showing that the existence of a coat structure that is highly resistant to degradative enzymes. Jessica Urbanczyk Mingyun Wang
Vangelisti A, Mascagni F, Giordani T, Sbrana C, Turrini A, Cavallini A, et al. (2019) Arbuscular mycorrhizal fungi induce the expression of specific retrotransposons in roots of sunflower (Helianthus annuus L.). PLoS ONE 14(2): e0212371. https://doi.org/10.1371/journal.pone.0212371 Commensalism Rhizoglomus irregulare Helianthus annuus L. Plants grown on moistened filter paper lied in Petri plates. Interaction happened on 90-mm diameter membrane (cellulose acetate-cellulose nitrate, 0.45 ?m pore diameter size, MF-Millipore), covered with a 100 cm2 nylon net (41 ?m mesh, Millipore), on a sterile 150-mm Petri plates containing steam-sterilised quartz grit, at 24C. Solid media, solution added, spatial Biofilm Continuous culture (nutrient added weekly) Aerobic Helianthus annuus L. root Natural Plating, RNA isolation, Reverse transcription, Single-read sequences of 100 bp length obtained by Illumina HiSeq 2000, Sequence mapping using CLCBio Genomics Workbench version 9.5.3, differential expression analysis Metabolic Yes The expression of retrotransposon induced by the colonization of fungi to plants Mingyun Wang
Hall, R. J., Flanagan, L. A., Bottery, M. J., Springthorpe, V., Thorpe, S., Darby, A. C., . . . Thomas, G. H. (2019). A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet. American Society for Microbiology,10(1). doi:10.1128/mbio.02106-18 ammensalism/parasitic - T. brucei is a pathogen Trypanosoma brucei Sodalis glossinidius in vitro on Defined Medium plates (SGM11): use of a carbon source lacking in the blood meal, namely, N-acetyl-d-glucosamine (GlcNAc). Plates were first created in silico to identify essential nutrients. Solid, well-mixed biofilm batch culture aerobic microbiome of the tsete fly (insert vector for the parasite) natural Flow Cytometry: Cell count was generated using S. glossinidius taken from a starter culture in BHI and diluted in M9 salts. Cells were stained with DAPI at 2??l/ml for 10 min at room temperature and measured on the CytoFLEX S flow cytometer metabolic no Alexandra Malarczyk Mingyun Wang
Hall, R. J., Flanagan, L. A., Bottery, M. J., Springthorpe, V., Thorpe, S., Darby, A. C., . . . Thomas, G. H. (2019). A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet. American Society for Microbiology,10(1). doi:10.1128/mbio.02106-18 commensalism Sodalis glossinidius Wigglesworthia glossinidia in vitro on Defined Medium plates (SGM11): use of a carbon source lacking in the blood meal, namely, N-acetyl-d-glucosamine (GlcNAc). Plates were first created in silico to identify essential nutrients. Solid, well-mixed biofilm batch culture aerobic microbiome of the tsete fly natural Flow Cytometry: Cell count was generated using S. glossinidius taken from a starter culture in BHI and diluted in M9 salts. Cells were stained with DAPI at 2??l/ml for 10 min at room temperature and measured on the CytoFLEX S flow cytometer metabolic: W. glossinidia provides thiamine for the unique vitamin auxotropy that S. glossinidius has no Alexandra Malarczyk Ashley Bodnar
Sommer, A. J., & Newell, P. D. (2018). Metabolic Basis for Mutualism between Gut Bacteria and Its Impact on the Drosophila melanogaster Host. Applied and Environmental Microbiology,85(2). doi:10.1128/aem.01882-18 mutualism Acetobacter fabarum Lactobacillus brevis in vitro coculture assay: Two 5-?l spots of mixed cultures were pipetted onto YPD agar plates containing 10?g/liter peptone, 10?g/liter yeast extract, 20?g/liter dextrose, and 15?g/liter agar. The plates were incubated for 6?days at 30C. solid agar, well-mixed biofilm batch cultures aerobic gut microbiota of Drosophila melanogaster natural plating/ genetic basis of both species using statistical analysis and genetic screens metabolic: A. fabarum genes required for enhanced growth with L. brevis, vidence that A. fabarum can utilize multiple fermentation products of L. brevis. Mutualism between the bacteria in vivo affects gnotobiotic Drosophila melanogaster no Alexandra Malarczyk Mingyun Wang
Mccully, A. L., Behringer, M. G., Gliessman, J. R., Pilipenko, E. V., Mazny, J. L., Lynch, M., . . . Mckinlay, J. B. (2018). An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris. Applied and Environmental Microbiology,84(14). doi:10.1128/aem.00404-18 mutualism Escherichia coli Rhodopseudomonas palustris All R. palustris strains contained ?uppE and ?hupS mutations to facilitate accurate CFU measurements by preventing cell aggregation and to prevent H2 uptake, respectively. E. coli was cultivated on Luria-Bertani (LB) agar, and R. palustris was cultured on defined photosynthetic medium (PM) agar with 10 mM succinate. (NH4)2SO4 was omitted from PM agar for determining R. palustris CFU. Monocultures and cocultures were grown in 10 ml of defined M9-derived coculture medium (MDC) (10) in 27-ml anaerobic test tubes under 100% N2; coculture consists of fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris solid agar, well-mixed biofilm batch cultures anaerobic soil, natural environment engineered transcriptome sequencing (RNA-seq) and proteomic analysis to determine changes in gene expression patterns/ mass spectrometry metabolic: In this coculture, E. coli anaerobically ferments glucose into organic acids, providing R. palustris with essential carbon. In return, a genetically engineered R. palustris strain (Nx) constitutively fixes N2 gas, resulting in NH4+ excretion that provides E. coli with essential nitrogen. The result is an obligate mutualism that maintains a stable coexistence and reproducible growth trends as long as bidirectional nutrient cross-feeding levels are maintained within a defined range. yes - see article, specifically Figure 2 Alexandra Malarczyk Seung Woo Kim
Bais, H. P., Fall, R., & Vivanco, J. M. (2004). Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant physiology, 134(1), 307-19. DOI: 10.1104/pp.103.028712 biocontrol Bacillus subtilis (strain 6051) Pseudomonas syringae pv tomato DC3000 B. subtilis and P. syrinage were first grown separately in liquid cultures and added to Arabidopsis to determine how the mircrobes intereacted with the plant roots on their own. This was done both when the plant roots were in culture and when the plant roots were in sterile soil. Then both species where added into liquid culture with the roots and in the sterile soil with the roots. The antibacterial activity of surfactin against P. syringae was determined in both broth and agar cultures and also by live-dead staining methods. well-mixed liquid culture, agar culture, as well as sterile soil biofilm aerobic B. subtilis and P. syrinage naturally live in soil near plant roots in vitro and in soil (both engineered) The overall health of the plant was observed. Cells were also analyzed by CSLM in order to determine if they were actually forming a biofilm and flouresence was used in order to determine which microbes were viable (tagged green) and which were dead (tagged red). It was observed the B. subtilis (specifically strain 6051) effectively formed biofilms around the roots of the plant and produced the surfactin, a lipopeptide antimicrobial agent that prevents P. syringae from forming an infectous biofilm. Otherwise, P. syringae would have formed its own biofilm around the roots to infect and kill the plant. This interaction was determined by comparing the interaction of P. syringae and B. subtilis strain 6051 to the interaction between P. syringae and B. subtilis mutat strain M1. M1 had a mutation in the surfactin synthase gene, making it an ineffective biocontrol agent against P. syringae. yes: (Figures 1-6 in paper. Invdividual links also included) Jessica Urbanczyk Claire McCann
Sztajer et al. 5 November 2018 Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans. Applied Microbiology and Biotechnology (2019) 103:731-745 https://doi.org/10.1007/s00253-018-9506-3 Mutualism Streptococcus mutans Candida albicans The pre-cultures of S. mutans and C. albicans were respectively grown in THBY medium with erythromycin and YNB medium supplemented with maltose and glucose both at 37C aerobically with 5% CO2 without shaking. S. mutans and C. albicans were inoculated from single colonies or frozen glycerol stocks, respectively, grown for 16 h, harvested by centrifugation and suspended in YNBB medium. Equal volumes of each strain (500 ml) were inoculated into the wells of 24-well microtitre plates. The plates were incubated aerobically (5% CO2) at 37C in pH 7.0 - 6.4. Biofilms were allowed to develop for 4, 6, 8, 10, 12 and 24 h. Well-mixed liquid culture Biofilm Batch Aerobic Oral cavity Natural Phase contrast microscopy was used to determine direct cell-cell contact. Scanning electron microscopy, gas chromatography-mass spectrometry and transcriptome analysis (microarray) was used to identify the presence of EPS matrix. When C. albicans is present, sucrose is taken up by C. albicans and no EPS is formed by S. mutans. Extracellular proteases of C. albicans could degrade S. mutans proteins and produce XIP, which is the main quorum sensing signal of S. mutans. XIP activates the transcriptional regulator comR, thereby triggering activation of the quorum sensing signalling cascade. ComR induces expression of the alternative sigma factor sigX, resulting in transcription of the transformasome genes and genetic competence of the cell. No Ryan Oleynik Seung Woo Kim
Help, hinder, hide and harm: what can we learn from the interactions between Pseudomonas aeruginosa and Staphylococcus aureus during respiratory infections competitive/cooperation (the interaction may vary at different stages of infection) Staphylococcus aureus Pseudomonas aeruginosa Isolated from the pulmonary/respiratory tract to study the related contribution of Staphylococcus aureus and Pseudomonas aeruginosa to cystic fibrosis and chronic airway diseases, including non-CF bronchiectasis, COPD and ventilator-associated pneumonia. In vitro cocultivation in animal models Biofilm in situ aerobic respiratory microbiota natural agar beads, culture-independent methods to quantitatively and longitudinally examine community dynamics of the CF airway microbiome during changes in clinical disease state, antimicrobial therapy and restoration of CF transmembrane conductance regulator (CFTR) activity Early P. aeruginosa isolates competitively exclude S. aureus during coculture, supporting the hypothesis that P. aeruginosa infection decreases the likelihood of S. aureus infection. P. aeruginosa also has the potential to produce an extensive arsenal of virulence determinants, which may be influenced by the presence of S. aureus during coinfection. Many of the virulence determinants previously discussed, which may provide P. aeruginosa a competitive advantage during growth with S. aureus, are also capable of inflicting significant collateral damage to the airway. A third microbe may also impact the interaction. no This article provides multiple examples on the interaction of these two microbes. Katie Piccioli Danielle Rinaldi
Interspecies Interactions within Oral Microbial Communities Howard K. Kuramitsu, Xuesong He, Renate Lux, Maxwell H. Anderson, Wenyuan Shi Parasitism Streptococcus mutans Streptococcus oligofermentans Isolated from dental plaque of human subjects In vitro competition assay, well-mixed culture Biofilm in situ aerobic oral cavity natural Plating - optical density analysis Lactic acid produced by S. mutans functions as a substrate for S. oligofermentans for H2O2 production No Typically, the mechanism for S. mutans inhibition of S. oligofermentan (and other acid-sensitive anaerobes) occurs due to lactic acid production. However, this study also found that H2O2 production limits growth of S. mutans. Danielle Rinaldi Amanda Bourne
Michelle Rubin, Amber D Miller, Mariko Katoh-Kurasawa, Christopher Dinh, Adam Kuspa, & Gad Shaulsky. (2019). Cooperative predation in the social amoebae dictyostelium discoideum. PLoS One, 14(1), e0209438. doi:10.1371/journal.pone.0209438 cooperation/prey-predation (both cheating and cooperation) Dictyostelium discoideum Dictyostelium discoideum Klebsiella pneumoniae and Staphylococcus aureus were first grown in liquid cultures (species were separated by culture) and were heat killed. The amobea were grown on these dead cells before being added with live bacteria. The amobea and the live bacteria were then transferred onto plates and incubated. liquid culture as well as agar plates planktonic cells batch aerobic Amoeba naturally live in warm water in rivers, lakes, or hot springs. They can also grow in pools that have not been properly chlorinated. engineered Allee effect anylysis (measuring cell density), fluoresence in order to count cells, and a synergy test which compares how two species interact with each other to how they would behave if they were in separate cultures Some D. discoideum mutants were able to synergize, but others were not, suggesting that cooperative predation also has a genetic compontent to it. The mutants that did synergize, however, grew at a more rapid pace that they did in their own pure cultures, suggesting cooperative predation. In addition, this study also tested whether or not cooperation would increase based on the production of a common good. Wildtpe D. discoideum was mixed with the mutants and it was observed that the wildtpe-mutant mix had a higher cell density than the mutant only culture, suggesting cooperation in growth. No While likely not considered to be raw data, this link provide supporting information/data, such asmore details about the strains used: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0209438#pone.0209438.s006 yes - table 1, figure 1 in paper
Zhongming Ge, Yan Feng, Sureshkumar Muthupalani, Laura Lemke Eurell, Nancy S. Taylor, Mark T. Whary, & James G. Fox. (2011). Coinfection with enterohepatic helicobacter species can ameliorate or promote helicobacter pylori-induced gastric pathology in C57BL/6 mice. Infection and Immunity, 79(10), 3861-3871. doi:10.1128/IAI.05357-11 amensalism Helicobacter pylori (strain SS1) Helicobacter hepaticus (strain 3B1 (ATCC 51449)) and Helicobacter muridarum (strain ST1 (ATCC 49282)) Mice were infected with H. pylori, H.pylori + H. hepaticus, or H. pylori + H. muridarum by ingestion. mouse gut (in vitro) planktonic cells in situ aerobic All species naturally live in their host gut/stomach/intestines natural (in vitro context) Tissue samples from the stomach were analyzed, real time quantitative PCR (Q-PCR) assay was used to determine colonization levels, and Immunohistochemistry for Fox3+ cells H. muridarum inhibits the colonization of H. pylori yes - table 1, figure 1, and figure 6 in paper Jessica Urbanczyk Seung Woo Kim
Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance commensalism Salmonella typhimurium (LT2) Escherichia coli (ancestral wild-type E. coli K-12 EMG2 +fertility factor plasmid (F+)) Treated exponential-phase S. typhimurium grown in tryptophan-free medium with a range of indole concentrations to determine the effect on tolerance to antibiotics that are used in clinical treatment of enteric Salmonella infections. Mixed an exponential-phase culture of S. typhimurium with a stationary-phase culture of E. coli grown in the presence of tryptophan to enable indole production to test if indole produced by E. coli in a mixed-microbial environment would also induce S. typhimurium tolerance. plated on selective media biofilm batch culture aerobic intestines engineered fluorescent microscopy, serial dilution, selective plating, quantitative PCR The intestinal pathogen S. typhimurium can intercept indole signaling from the commensal bacterium E. coli to enhance its antibiotic tolerance in the host intestine. yes - https://www.pnas.org/content/110/35/14420/tab-figures-data The antibiotic tolerance of S. typhimurium is mediated, in part, by oxidative stress and phage shock response systems. Katie Piccioli Danielle Rinaldi
Mixed-Culture Interactions I. Commensalism of Proteus vulgaris with Saccharomyces cerevisiae in Continuous Culture (Adnan Shindala, Henry R. Bungay, III, Noel R. Krieg, Kathleen Culbert) commensalism (a competitive situation is also possible when the fast-growing bacterium benefit at the expense of the yeast until the substrate dilutes again) Proteus vulgaris Saccharomyces cerevisiae Concentrated stock solutions of the salts, of glucose, and of the vitamins were autoclaved separately at 15 psi for 20 min and then combined aseptically, after cooling, to form the complete medium. Yeast extract, niacin, and related compounds to be added to steady-state mixed cultures were dissolved in water, sterilized by filtration, and stored at -25 C until use. S. cerevesiae is prepared on potato dextrose agar and P. vulgaris is prepared on tryptic soy agar, and they are grown in batch cultures before the continuous medium addition phase. steady-state mixed culture N/A continuous culture aerobic N/A engineered Steady-state populations of each organism in mixed culture at various dilution rates were enumerated with a Coulter electronic counter. The size differences in the organisms permitted easy resolution. An essential niacinlike factor elaborated by the yeast and required by the bacterium caused a dependence of the bacterium on the growth of the yeast. At high dilution rates causing wash-out, the bacterial population continued to reflect changes in the numbers of yeast. no Katie Piccioli Amanda Bourne
Microbial interactions in the vaginal ecosystem, with emphasis on the pathogenesis of bacterial vaginosis Commensalism Prevotella bivia Gardnerella vaginalis Vaginal defined medium, various pH levels tested (6.0-7.5) Solid media; tests were also run in liquid media were unsuccessful biofilm Continuous culture Aerobic Vaginal cavity Natural Growth comparisons (length of lag phase, etc.) between controlled media and defined media with the full microbial community Ammonia flow from P. bivia to G. vaginalis provides nutrients to the latter while removing potentially toxic byproducts for the former. In vivo analysis of the microbial communities of both pregnant and non-pregnant women demonstrates the importance of H2O2 in control of these two microbes. No Danielle Rinaldi Katie Piccioli
Jia, T.; Wang, J.; Chang, W.; Fan, X.; Sui, X.; Song, F. Proteomics Analysis of E. angustifolia Seedlings Inoculated with Arbuscular Mycorrhizal Fungi under Salt Stress. Int. J. Mol. Sci. 2019, 20, 788. doi:https://doi.org/10.3390/ijms20030788 Commensalism Rhizophagus irregularis E. angustifolia Pots containing the seedlings were inoculated with active or inactive Rhizophagus irregularis; Salt was added after 4 months of inoculation; Pots were put under outdoor natural environment for the experiment. Solid media, spatial Biofilm batch culture Aerobic N/A Engineered Acid fuchsin staining method for colonization rate detection; authrone colorimetric method and coomassie brilliant blue G-250 method to measure sugar and soluble protein contents as indicator of salt stress; Protein extracts were quantified with BCA Protein Assay Kit; FASP Digestion; LC-MS/MS Analysis; Protein GO Functional Annotation and KEGG Pathway Annotation; Protein-Protein Interact Network (PPI) Metabolic (Rhizophagus irregularis inoculated E. angustifolia seedlings increased secondary metabolism, enhanced Ca2+ signal transduction and ROS scavenging capacity, promoted protein biosynthesis, accelerated protein folding, and inhibited protein degradation compared with non-inoculated plants under salt stress) Yes Mingyun Wang
Interspecies Social Spreading: Interaction between Two Sessile Soil Bacteria Leads to Emergence of Surface Motility. (McCully LM, Bitzer AS, Seaton SC, Smith LM, Silby MW) mutualism (interspecies social spreading) Pseudomonas fluorescens Pf0-1 Pedobacter sp. strain V48 P. fluorescens and Pedobacter for use in social spreading assays were incubated in 2?ml TSB-NK at 20C for 24 h, with shaking (160?rpm). Social spreading assays were carried out on TSB-NK solidified with 2% agar. Plates were poured at a temperature of -62C in a single layer and allowed to set for ?15 min before inoculation. Inoculation was done on freshly poured plates. solid media, well-mixed biofilm batch culture N/A Soil engineered Mixed inoculum assays, direct contact assays (adjacent plating and separation by membranes), cellophane overlay assays, and heat kill assays were carried out on TSB-NK solidified with 2% agar and inoculation was done. The nutritional environment influences social spreading: no social behavior is observed under high-nutrient conditions, but low-nutrient conditions are insufficient to promote social spreading without high salt concentrations. When grown in isolation, neither species moves beyond the typical amount of colony expansion. In coculture, both bacteria are present throughout the spreading colony, and fluorescent imaging shows a nonhomogenous distribution. The statistic comparisons measured colony diameter and movement based on fluorescent tags helped to to analyze social spreading. Contact dependent: a close association between the colonies of the two species is required for interspecies social spreading to initiate. The social phenotype could be observed only under specific nutritional conditions, indicating an interplay between environmental and biological factors. Yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354810/ Katie Piccioli Amanda Bourne
Zhang, Lei, Yuko Narita, Lin Gao, Muhammad Ali, Mamoru Oshiki, Satoshi Ishii, and Satoshi Okabe. 2017. Microbial Competition among Anammox Bacteria in Nitrite-Limited Bioreactors. Vol. 125. doi://doi.org/10.1016/j.watres.2017.08.052. doi: http://www.sciencedirect.com/science/article/pii/S0043135417307145. Competition Candidatus Brocadia sinica Candidatus Jettenia caeni gel-immobilizedcells in up-flow column reactors, planktonic free-living cells in MBR, and self-aggregated granules in an up-flow column reactor; inorganic nutrient medium was added continuously, with three different nitrogen loading rate; mixture of bacteria were inoculated well-mixed Planktonic immobolized, planktonic, and self-aggregated for three experiments Continuous culture Anaerobic N/A Natural Concentrations of NH4+, NO2-, and NO3- analyzed using ion-exchange chromatography, with a Ionpac CS3 cation column and Ionpac AS9 anion column; DNA extraction; TaqMan qPCR assay; Fluorescence in situ hybridization (FISH) used to analyze the spatial distribution of each species "C. J. caeni" could proliferate only at low NLRs, whereas "Ca. B. sinica" outcompeted the other species at hight NLRs in both bioreactors. Yes Mingyun Wang Claire McCann
van Gils, Stijn et al. Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer. PloS one vol. 12,8 e0179695. 17 Aug. 2017, doi:10.1371/journal.pone.0179695 Commensalism Rhizoctonia solani Sitobion avenae S. avenae are grown on wheat in the presence of sterilized soil with two levels of soil organic matter, high or low fertilizer supply, and in the presence or absence of 5 mm plugs of R. solani, which grew for a week on a Petri dish with 1/5th Potato Dextrose Agar spatial biofilm batch culture aerobic soil natural 3 weeks after development, the S. avenae were infested into the pots, and removed four weeks later. They were weighed and one week later the plants they grew on were harvested, oven dried, and weighed. The shoot plant material was grinded to a powder and dried again to measure carbon and nitrogen concentration, to see how the R. solani affected the concentrations. In soil with low organic matter content, R. solani decreased biomass of S. avenae and increased it in soil with high organic matter content. no Claire McCann Ashley Bodnar
Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell-cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography doi: 10.1007/s00203-008-0402-6 Contact sites. generation of filaments. (The possible function of the cytoplasmic filaments observed remains unclear) Ignicoccus hospitalis Nanoarchaeum equitans The type strain I.hospitalis KIN4/IT was obtained from the Culture Collection of the Institute for Microbiology and Archaea Centre, University of Regensburg. Cells were grown in SME medium at 90C, as described (Huber et al. 2000; Paper et al. 2007), with elemental sulphur as electron donor and a gas phase consisting of H2/CO2 (250 kPa; 80/20, v/v). Solid and liquid media. mixed. suspesions; Planktonic Batch Culture collected anaerobically N/A (I.Hospitalis is an anaerobic hyperthermophilic chimolithoautotroph) engineered Ultrastructure and intercellular interaction of Ignicoccus hospitalis and Nanoarchaeum equitans were investigated using two different electron microscopy approaches, by three-dimensional reconstructions from serial sections, and by electron cryotomography. Micrographs of about 120 contact sites, in total were collected. For only ~30 of these, sample preservation, section plane and image quality were satisfactory in order to deduce structural information. The electron micrographs of cell contact sites were analysed especially for two aspects: the organization of the two I. hospitalis membranes, in particular the gap in between, and the gap between the two cell surfaces. One is indirect and mediated by thin fibres; in other cells the two cell surfaces are in direct contact. The two membranes of I. hospitalis cells are frequently seen in direct contact, possibly a prerequisite for transporting metabolites or substrates from the cytoplasm of one cell to the other. yes (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755780/) the same link has all of the raw data N. equitans cells cannot be cultivated alone but only in the presence of and in contact with living I. hospitalis cells. With only ~0.49 Mbp, the N. equitans genome is the smallest of all Archaea known today; it lacks genes for the biosynthesis of lipids, amino acids, nucleotides and cofactors (Waters et al. 2003). There is experimental evidence that lipids (Jahn et al. 2004) and amino acids (Jahn et al. 2008) are transported from I. hospitalis to N. equitans. Jude Aboukhater Claire McCann
Pais, Ines S et al. Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria. PLoS biology vol. 16,7 e2005710. 5 Jul. 2018, doi:10.1371/journal.pbio.2005710 mutualism Drosophila melanogaster Acetobacter thailandicus Wild flies (D. melanogaster) were caught in the wild, the guts were digested and ground up, and each centrifuge tube consisted of the ground up gut in 250 microliters of Lysogeny Broth (LB). Each sample was serially diluted and 30 microliters was placed on 5 different plates, LB, Rogosa and Sharpe broth, Liver infusion broth, brain heart infusion, and mannitol. Plates were incubated at 25 degrees for 6 days, and bacteria was isolated and counted solid and liquid media biofilm planktonic in fly gut continuous aerobic fly gut natural A PCR to amplify to 16S rRNA gene was performed to identify each isolated bacteria. The bacterial level in each fly was then analyzed using the Mann-Whitney test, and bacterial concentrations were calculated using OD600 with a spectrophotometer. Flies inoculated with A. thailandicus had a higher fertility rate, and both parents passed the benefits to their children. Also, the eggs of flies with A. thailandicus developed faster than without. Also, A. thailandicus is transmitted at a higher rate than other bacteria when colonizing flies. no Claire McCann Aidan Pavao
Martin B, Tamanai-Shacoori Z, Bronsard J, Ginguen F, Meuric V, Mah F, et al. (2017) A new mathematical model of bacterial interactions in two-species oral biofilms. PLoS ONE 12(3): e0173153. https://doi.org/10.1371/journal.pone.0173153 Commensalism Porphyromonas gingivalis Streptococcus gordonii P. gingivalis and S. Gordonii were inoculated and grown on Columbia blood agar (solid media) and in a brain-heart broth (liquid media). The samples were taken from new colonies, diluted, and incubated in an anaerobic setting. The growths were studied during their log phases. Solid and liquid media Biofilm batch Anaerobic Mouth Natural Biofilm development predicted using a mathematical model, growths were analyzed using confocal scanning microscopy, fluorescent spectroscopy, and RT-PCRq P. gingivalis turns natural biofilms of bacteria like S. gordonii into pathogens that cause the disease periodontitis, creating a dysbiotic environment from an otherwise healthy one. no Daniel Garvey Alexandra Malarczyk
Wang, N., Wang, L., Zhu, K., Hou, S., Chen, L., Mi, D., Gui, Y., Qi, Y., Jiang, C., Guo, J. H. (2019). Plant Root Exudates Are Involved in Bacillus cereus AR156 Mediated Biocontrol Against Ralstonia solanacearum. Frontiers in microbiology, 10, 98. doi:10.3389/fmicb.2019.00098 Ammensalism Bacillus cereus Ralstonia solanacearum B. cereus was isolated from forest soil in Zhenjiang City, China, and then were grown either in a LB medium at 30 degrees on an agar plate or for 24 hours in a liquid medium. R. solanacearum was isolated from ingected tomato plants and were grown either on a YGPA medium at 28 degrees C on solid plates or for 24 hours in a liquid medium. Solid and Liquid Media Planktonic Cells and Biofilm; the biofilm was formed with the aid of fructose, lactic acid, D-pinitol, sucrose, threonine, and hexanoic acid. Batch Culture Aerobic Soil Engineered Plating was used to determine the relative growth increment of the bacterial species. Similar experiments using plating determined the bacterial motility and antagonism ability of the interaction. Finally, tomato seeds were grown in soil, and B. cereus culture was added. A week later, R. solanacearum was drenched into the pots, to determine the disease incidence after the pathogenic inoculation. The baterium B. cereus is found in plants and has a positive effect on biocontrol against many plant diseases using a metabolic mechanism. Yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365458/ Sarah Ryan Claire McCann
Schifano, E.; Zinno, P.; Guantario, B.; Roselli, M.; Marcoccia, S.; Devirgiliis, C.; Uccelletti, D. The Foodborne Strain Lactobacillus fermentum MBC2 Triggers pept-1-Dependent Pro-Longevity Effects in Caenorhabditis elegans. Microorganisms 2019, 7, 45. Commensalism Lactobacillus fermentum Caenorhabditis elegans L. fermentum were grown in an MRS medium for 24-48 hours at 37C under anaerobic conditions. C. elegans were bred on peptone-free nematode growth medium (NGM), and were fed L. fermentum. Then 25 microliters of each culture was resuspended in M9 buffer and was spread on mNGM plates, allowing the nematodes to produce colony forming units. Solid Media Biofilm Batch Culture Anaerobic L. fermentum is nautrally in the gastrointestinal tract and can be used as a starter culture for food fermentation processes, such as for cheese and sourdough. In this experiemnt, it was isolated from Mozzarella di Bufala Campana, an Italian cheese. C. elegans is a nematode that is found in temperature soil environments. Engineered The interaction occurred on the mNGM agar plates, and each trial lasted for 48 hours. The C. elegans were matured 5 days into adulthood, and were provided with L. fermentum, with the aim to stimulate growth of the C. elegans and have beneficial effects on their gut microbiota. These effects include protection against pathogenic bacteria, and prevention from disease, which were reliant on the ability of the L. fermentum strain to remain viable throughout the course of the experiment. The beneficial effects are a result of the ability of L. fermentum to survive within the GI tract despite it being a low pH environment. L. fermentum uses a resource-competition mechanism as it interacts with the preexisting microbes in the C. elegans gut. Yes https://www.mdpi.com/2076-2607/7/2/45/htm Sarah Ryan Alexandra Malarczyk
Kruppa, M. D., Jacobs, J., King-Hook, K., Galloway, K., Berry, A., Kintner, J., Whittimore, J. D., Fritz, R., Schoborg, R. V., Hall, J. V. (2019). Binding of Elementary Bodies by the Opportunistic Fungal Pathogen Candida albicans or Soluble Glucan, Laminarin, Inhibits Chlamydia trachomatis Infectivity. Frontiers in microbiology, 9, 3270. doi:10.3389/fmicb.2018.03270 Commensalism Candida albicans Chlamydia trachomatis C. albicans cultures were kept at 30 degrees C in YPD, then transferred to medium 199. C. trachomatis cells were grown in bead culture. After the C. albicans were cultured for 3-6 hours, they were mixed with C. trachomatis and plated onto coverslips. After incubation, they were washed, given new medium and incubated for 24 hours. Liquid Culture and Solid Media Planktonic Cells and Biofilm Batch Culture Aerobic C. albicans is typically found in the oral and vaginal microbiota responsible for thursh and yeast infections. They are a form of yeast that grows rapidly, causing such an infection. C. trachomatis is a bacterial pathogen that causes a sexually transmitted infection, often found in the human genitalia. This pathogen can also spread throughout the human body, causing inflammatory disease and infertility. Engineered The interaction occurred when the two species were plated onto coverslips. The C. albicans was cultured and incubated prior at 37 degrees C, so that hyphal formation could occur. The two species were incubated at 35 degrees C for 10 hour, then washed and fixed with methanol, formaldehyde or glutaraldehyde. The C. trachomatis was observed for its growth on the C. albicans hyphae, and the results indicated the conditions for optimal growth. C. trachomatis uses a resource-competition mechanism to grow on the hyphae formed by the yeast C. albicans. Yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339894/ This study proved that a Candida albicans colonization does not always impact Chlamydia trachomatis infections in vivo. These types of infections are not affected in every patient becuase of the potential presence of other facotrs in the body, including seminal fluid and vaginal secretions. This could be an environmental problem, in which the conditions did not allow the infection to be elimiated. This may also be because even with the direct interaction between the C. albicans and elementary bodies during the experiment, it still prohibited a decrease in the prevalence of the Chlamydia infection. Sarah Ryan Alexandra Malarczyk
Mendes, F., Sieuwerts, S., de Hulster, E., Almering, M. J., Luttik, M. A., Pronk, J. T., Smid, E. J., Bron, P. A., Daran-Lapujade, P. (2013). Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures. Applied and environmental microbiology, 79(19), 5949-61. Cooperation Saccharomyces cerevisiae Lactobacillus delbrueckii S. cerevisiae were grown on YPD medium and grown to the stationary phase at 30 degrees C. L. delbrueckii was also grown to its stationary phase at 37 degrees C on a MRS medium. During the interaction, the bulgaricus cerevisiae medium was used to provide the nutrients for both microbes. Solid Media Planktonic Cells Batch Culture and Continuous Culture Anaerobic S. cerevisiae naturally occurs in dairy, food, and beverage fermentations. The species used in this experiment, as well as L. delbrueckii, are found in kefir fermentations. Engineered The interaction occurred on plates, and the growth was observed on these. Additionally, the researchers used liquid chromatography to analyze the supernatant. They used this technique as well as gas chromatography-mass spectrometry to measure the free amino acids in the sample. [1] L. delbrueckii hydrolyzes lactose to galactose and glucose. S. cerevisiae uses galactose. [2] L. delbrueckii only grows with increased CO2, which yeast provides in anaerobic conditions. [3] S. cerevisiae provides alanine to bacteria. [4] chelation of Fe by lactate from L. delbrueckii. [5] L. delbrueckii overrepresents transcripts for lipid metabolism. Yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811385/ Sarah Ryan Alexandra Malarczyk
Chen M, Wolin MJ. Influence of CH4 production by Methanobacterium ruminantium on the fermentation of glucose and lactate by Selenomonas ruminantium. Appl Environ Microbiol. 1977;34(6):756-9. Mutualism Methanobacterium ruminantium Selenomonas ruminantium The Hungate technique was used for media prep. liquid culture planktonic cells batch culture anaerobic Rumen of animals Natural gas chromatography, Somogyi procedure, glucose oxidase procedure (Sigma Chemical Co.), formyltetrahydrofolate synthetase method (Rabinowitz and Pricer), alcohol dehydrogenase method (Bonnichsen), lactic acid method (Barker Summerson) Methane production of M. ruminantium impacts fermentation of S. ruminantium No Glucose fermentation by S. ruminantium alone favored lactate production. Sequential transfers with M. ruminantium was correlated with a decrease in lactate production, however, and was also correlated with an increase in acetate. Addition of the methnogen also decreased propionate production. Declan Ryan Daniel Garvey
Vogels GD, Hoppe WF, STumm CK. Association of methanogenic bacteria with rumen ciliates. Appl Environ Microbiol 1980;40(3):608-12 Mutualism 11 species of rumen ciliates of the family Ophryoscolecidae (see Table 1) Varied methanogenic bacteria (Streptococcus bovis, Ruminococcus albus) Rumen contents were collected after slaughter of each cow, and microscopy was performed with Leitz Dialux microscope liquid media planktonic cells in situ anaerobic Rumen of animals Natural Bright-field and epifluorescence microscopy Somatic (attachment) and metabolic transfer of hydrogen Imaging available https://www.ncbi.nlm.nih.gov/pmc/articles/PMC291627/pdf/aem00239-0188.pdf While unclear, it is possible individual cow diet, availability of energy sources, and environmental nitrogen could contribute to the variety of interaction frequencies. Declan Ryan Daniel Garvey
Park T, Yu Z. Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?. Front Microbiol. 2018;9:1710. Published 2018 Jul 31. doi:10.3389/fmicb.2018.01710 Predator-Prey and Symbiotic Various rumen ciliates inc. Entodinium caudatum and Epidinum caudatum Various bacteria: Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, Proetbacteria Monoculture: The monocultures of Ent. caudatum and Epi. caudatum used in the present study were initially established from single cells individually picked from the rumen fluid of a gerenuk and a Jersey dairy cow, respectively (Dehority, 2010) Fresh isolate: Fresh rumen fluid samples were collected 2 h after morning feeding from 5 rumen-cannulated Jersey dairy cows, which were fed a total mixed ration consisting of corn silage, alfalfa hay, and grounded shelled-corn. Laboratory monoculture in SP medium at 39C and maintained by transfer twice a week; fresh rumen fluid planktonic cells aerobic anaerobic Rumen of animals Natural Illumina MiSeq sequencing and analysis, quantitative PCR (qpCR) Rumen ciliates lower nitrogen utilization efficiency in ruminants by decreasing microbial protein supply to the host small intestine ue to constant engulfing of bacteria and subsequent bacterial protein degradation inside the rumen(Fondevila and Dehority, 2001) No This study IDs a number of CAPs (ciliate associated prokaryotes) for the first time. Various species were detected and ID'd as FLPs/CAPs (see species 2) Declan Ryan Daniel Garvey
S. Kisidayov,a P. Houserove,b Z. Varadyova,a K. Mihalikova,a P. Prista,a P. Javorska. Bacterial-protozoal interactions in a microbial community of rumen ciliate Entodinium caudatum culture under mercury stress Can. Journ. Microbiol (2010) 56(3): 202-208 commensalism Entodinium caudatum mixed bacteria E. caudatum was isolated form sheep rumen and grown in basic mineral culture medium supplemented with microelements under anaerobic conditions at 39.5C for 6 months. The basic mineral culture medium was a caudatum-type medium as described by Williams and Coleman (1992) liquid culture planktonic cells continuous culture anaerobic rumen of animals Natural The researchers compared cultures of E. caudatum growing in the presence of mercury with other cultures of E. caudatum with added ruminal bacteria. Rumen bacteria transformed mercury (II) into its insoluble forms, protecting protozoal cells from mercury toxicity. No Not curated Declan Ryan
Roth, B., Twiner, M., Mikulski, C., Barnhorst, A., Doucette, G. (2008). Comparative analysis of two algicidal bacteria against the red tide dinoflagellate Karenia brevis. Elsevier Harmful Algae, 7(5), 682-691. https://doi.org/10.1016/j.hal.2008.02.002 amensalism Karenia brevis C2 Cytophaga/Flavobacterium/Bacteroidetes (CFB)-bacterium, strain S03 and strain 41-DBG2 water samples collected from three depths from the west Florida shelf that were filtered, amended with glycerol, and then stored in liquid nitrogen liquid culture planktonic cells continuous culture aerobic freshwater and seawater Can occur naturally, but this experiment was engineered to test what effects different strains of bacteria had on K. brevis C2 in vivo fluorescence CFB-bacteria strains cause the formation of a small number of cyst-like structures and eventually cell lysis of K. brevis C2 strains No Strain S03, when introduced, showed an immediate decline in K. brevis C2 cultures - complete cell lysis shortly after at Day 5 - Strain 41-DBG2 showed lysis of K. brevis C2 cultures at Day 7 Ashley Bodnar
Yoneda, M., Yoshikane, T., Motooka, N., Yamada, K., Hisama, K., Naito, T. Okada, I. Yoshinaga, M., Hidaka, K., Imaizumi, K., Maeda, K., Hirofuji, T. (2005). Stimulation of growth of Porphyromonas gingivalis by cell extracts from Tannerella forsythia. Journal of Periodontal Research, 40(2), 105-109. https://doi.org/10.1111/j.1600-0765.2005.00774.x commensalism Porphyromonas gingivalis Tannerella forsythia P. gingivalis and T. forsythia were isolated from active periodontitis sites - T. forsythia was added to nutrition-decreased medium and the promotion of growth of P. gingivalis was examined liquid culture biofilm batch culture aerobic oral cavity natural 100 ul of P. gingivalis suspension was inoculated into 5 ml of diluted tryptic soy broth, with or without bacterial cell extracts. Diluted tryptic soy broth supplemented with bacterial cell extracts was incubated at the same time and served as a blank T. forsythia stimulates growth of P. gingivalis under nutrition-limited conditions No Growth promotion by T. forsythia was only evident at the early stages of growth. Using heat treatment showed a decrease in the growth-promoting effect Ashley Bodnar Patrick Lima
Chien, Y., Vidal, J., Grijalva, C., Bozio, C., Edwards, K., Williams, J., Griffin, M., Verastegui, H., Hartinger, S., Gil, A., Lanata, C., Klugman, K. (2013). Density Interactions between Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus in the Nasopharynx of Young Peruvian Children. The Pediatrics Infectious Disease Journal, 32(1), 62-71. doi: 10.1097/INF.0b013e318270d850 cooperation Streptococcus pneumoniae Haemophilus influenzae (NTHi) a cohort of ~500 children 0-35 months of ages in the District of San Marcos, Cajamarca, Peru - nasopharyngeal swabs for bacterial colonization were collected monthly on all children using Rayon swabs immediately placed in 1 mL of transport medium (skim-milk tryptone glucose glycerol, STGG) liquid culture biofilm continuous culture aerobic nasopharynx natural qPCR and Spearman correlation coefficients, after collection the different cultures recieved various different enrichment broths and incubated with specific conditions The densities of S. pneumoniae and H. influenzae, measured by qPCR, were positively correlated, however the mechanism by which S. pneumoniae and H. influenzae influence each other in the nasopharynx is complex and may be affected by which one initially colonized the nasopharynx No Many studies have been done, with each yielding different results, so it is difficult to come up with a conclusion based on the interactions between S. pneumoniae and H. influenzae. S. aureus could also be studied to understand this interaction. Ashley Bodnar Declan Ryan
Wen, T., Liao, S., Bitoun, J., De, A., Jorgensen, A., Feng, S., Xu, X., Chain, P., Caufield, P., Koo, H., Li, Y. (2017). Streptococcus mutans Displays Altered Stress Responses While Enhancing Biofilm Formation by Lactobacillus casei in Mixed-Species Consortium. Frontiers in Cellular and Infection Microbiology, 7(524), 1-12. doi: 10.3389/fcimb.2017.00524 It appears to be commensalism, however, this cannot be confirmed unless planktonic numbers data is also observed Streptococcus mutans Lactobacillus casei For continuous flowing conditions, S. mutans and L. casei were grown in mFMC with glucose (18mM) and sucrose (2mM), and biofilms were grown on glass slides deposited in a Drip Flow Biofil Reactor. The system was run with a medium flow rate of 60 ml per hour in a 37C warm room for 48 and 120 h, respectively. solid media biofilm continuous culture aerobic oral cavity natural The biofilms were scratched off with a sterile spatula and suspended in 5 mL of potassium phosphate buffer, sonicated briefly to de-chain and separate the cells, and serial dilutions were then plated in triplicate on proper agar medium for enumeration of viable biofilm cells S. mutans possesses at least three Gtf enzymes that produce glucose polymers from sucrose, playing a central role in bacterial adherence and biofilm accumulation - this allows L. casei to form a better biofilm than it can on its own No Lactobacilli when grown on their own, have difficulty growing biofilms, L. casei grown with S. mutans increased its biofilm by 54-fold Ashley Bodnar Jude Aboukhater
Interaction of Candida albicans with an Intestinal Pathogen, Salmonella enterica Serovar Typhimurium Emmanouil Tampakakis, Anton Y. Peleg, Eleftherios Mylonakis Eukaryotic Cell May 2009, 8 (5) 732-737; DOI: 10.1128/EC.00016-09 antagonistic Candida albicans (fungus) Salmonella enterica Serovar Typhimurium(bacteria) The original samples of S. typhimurium were grown in LB broth and then were selected from LB agar(solid) containing antibiotics and C. albicans were grown in YPD broth and were later selected from YPD agar. C. elegans (nematodes) were infected with the C. ablican, which was allowed to grow for 4 hours and then was transfered into a liquid broth that contained the S. typhimurium and the growth of the fungus and viability of the nematodes were observed to conclude that the S. typhimurium impedes the growth of the C. albican. This was performed in an earlier study and then this study focused on studying how this relationship was functioning at different temperatures in the in vitro planktonic cultures and in the biofilm. The planktonic cultures were grown at 30 degrees Celsius and 37 degrees Celsius. The biofilm cultures were grown on a silicon pad assay and exposed to filter-sterilized filtrate from the S. typhimurium with spider medium. liquid cultures planktonic and biofilm growth observed batch(original cultures)/in situ (when in nematodes) anaerobic gastrointenstinal tract (gut) natural Imaging and confocal microscropy were used to observe the growth pattern and viability of the cells in the cultures as well as in the nematodes. The S. typhurium prevents the filamentation of the C. alblican, reducing its viability and ability to form biofilms, through the secretion of a quorum sensing molecule. The growth of the S. typhurium bacteria depends on the inhibition of the filamentation of its competitor for space and resources. Yes , see listed source The growth of both species were tested at 30 degrees Celsuis(comparable to the temperature of the nematode gut environment) and 37 degrees Celsius (comparable to human body temperature) to demonstrate that this interaction is not dependent on organism. Amanda Bourne Katie Piccioli
Pseudomonas-Saccharomyces Interactions: Influence of Fungal Metabolism on Bacterial Physiology and Survival Julia D. Romano, Roberto Kolter DOI: 10.1128/JB.187.3.940-948.2005 mutualism Pseudomonas putida Saccharomyces cerevisiae P. putida isolated from soil by resuspending soil in distilled water and then plating on cetrimide agar and isolated into single colonies. S. cerevisiae and P. putida incubated together in different YP media solid media/liquid culture biofilm batch/in situ aerobic Soil/plants natural Grapes and grape juice were used to provide an environment where the two microbes may interact in nature. The two microbes were also grown on cellophane and separated to see whether or not the two had to be in direct contact in order for beneficial effects to be observed. The presence of a fungus, S. cerevisiae proved beneficial for the the growth of a bacterial strain, P. putida, and vice versa. They were shown to cooperate when placed in a natural environment where they could potentially interact in nature (grapes and grape juice) and were found to be beneficial for each other's growth. It was found that direct contact between fungus and bacteria is not necessary to observe effects. Metabolic no Daniel Garvey Ashley Bodnar
Nogueira, M. F., Pereira, L., Jenull, S., Kuchler, K., & Lion, T. (2019). Klebsiella pneumoniae prevents spore germination and hyphal development of Aspergillus species. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36524-8 Antagonism Aspergillus terreus Klabsiella pnuemoniae (ATCC13883 and ATCC700603) For qualitative assessment of bacterial-fungal interaction, Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium at 37C. For co-culture experiments, fungi and bacteria were either mixed at time zero or K. pneumoniae strains were added after pre-germination of Aspergillus spores. solid media (Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium (Formedium, Norfolk, UK) at 37C. biofilm batch aerobic lungs and intestines natural The level of inhibition of fungal spore germination was assessed by qPCR at 24?h and imaged by confocal microscopy (to measure the biofilm thickness the Aspergillus spp). K. pneumoniae is able to prevent Aspergillus species spore generation and hyphal interaction and is dependent on direct interaction with metabolically active bacteria as evidened by the reversibility of this inhibition. The exact mechanism for these effects is not known with certainty. no Patrick Lima Seung Woo Kim
Nogueira, M. F., Pereira, L., Jenull, S., Kuchler, K., & Lion, T. (2019). Klebsiella pneumoniae prevents spore germination and hyphal development of Aspergillus species. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36524-8 Antagonism Aspergillus niger Klabsiella pnuemoniae (ATCC13883 and ATCC700603) For qualitative assessment of bacterial-fungal interaction, Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium at 37C. For co-culture experiments, fungi and bacteria were either mixed at time zero or K. pneumoniae strains were added after pre-germination of Aspergillus spores. solid media (Aspergillus spp. and K. pneumoniae were grown alone and in co-culture in sterile-filtered yeast extract peptone dextrose (YPD) medium (Formedium, Norfolk, UK) at 37C. biofilm batch aerobic lungs and intestines natural The level of inhibition of fungal spore germination was assessed by qPCR at 24?h and imaged by confocal microscopy (to measure the biofilm thickness the Aspergillus spp). K. pneumoniae is able to prevent Aspergillus species spore generation and hyphal interaction and is dependent on direct interaction with metabolically active bacteria as evidened by the reversibility of this inhibition. The exact mechanism for these effects is not known with certainty. no Inhibition is independent of the Aspergillus species. Patrick Lima Sophia Al-Shwauva
Guevara-Avendao, E., Bejarano-Bolivar, A. A., Kiel-Martinez, A.-L., Ramirez-Vazquez, M., Mendez-Bravo, A., von Wobeser, E. A., Reverchon, F. (2019). Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides. Microbiological Research, 219, 74-83. https://doi.org/10.1016/j.micres.2018.11.009 Antagonism Bacillus velezensis Fusarium solani Briefly, each bacterial isolate (n = 45) was streaked to prepare a bacterial lawn onto a base plate containing LB medium (Chaurasia et al., 2005; Gao et al., 2017). Lids were removed and replaced by another base plate containing in its center a disc of 5 mm diameter of fungal mycelium on PDA. Both base plates were sealed with Parafilm and incubated for seven days at 30C. Each bacterial isolate was tested for antifungal activity in triplicate. Three assays were set up without bacterial treatments (LB only) and used as controls. Solid Biofilm batch culture aerobic avocado plant roots engineered Confocal laser scanning microscopy and scanning electron microscopy were used to calculate the percentage of mycelia growth inhibition (by coomparing the diameter of fungal mycelial growth in the control versus when the fungus was allowed to interact with the bacteria spp.) Metabolic (bacterial volatile organic compounds known as VOC's such as ketone, pyrazines and sulfur-containing compounds were found to reduce mycelial growth in particular fungal species) no Patrick Lima Ryan Oleynik
Guevara-Avendao, E., Bejarano-Bolivar, A. A., Kiel-Martinez, A.-L., Ramirez-Vazquez, M., Mendez-Bravo, A., von Wobeser, E. A., Reverchon, F. Change to Guevara-Avendao et el. (2019). Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides. Microbiological Research, 219, 74-83. https://doi.org/10.1016/j.micres.2018.11.009 Antagonism Bacillus velezensis Colletotrichum gloeosporioide Briefly, each bacterial isolate (n = 45) was streaked to prepare a bacterial lawn onto a base plate containing LB medium (Chaurasia et al., 2005; Gao et al., 2017). Lids were removed and replaced by another base plate containing in its center a disc of 5 mm diameter of fungal mycelium on PDA. Both base plates were sealed with Parafilm and incubated for seven days at 30C. Each bacterial isolate was tested for antifungal activity in triplicate. Three assays were set up without bacterial treatments (LB only) and used as controls. Solid Biofilm batch culture aerobic avocado plant roots engineered Confocal laser scanning microscopy and scanning electron microscopy were used to calculate the percentage of mycelia growth inhibition (by coomparing the diameter of fungal mycelial growth in the control versus when the fungus was allowed to interact with the bacteria spp.) Metabolic (bacterial volatile organic compounds known as VOC's such as ketone, pyrazines and sulfur-containing compounds were found to reduce mycelial growth in particular fungal species) no Patrick Lima Joan Donahue
Guevara-Avendao, E., Bejarano-Bolivar, A. A., Kiel-Martinez, A.-L., Ramirez-Vazquez, M., Mendez-Bravo, A., von Wobeser, E. A., Reverchon, F. (2019). Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides. Microbiological Research, 219, 74-83. https://doi.org/10.1016/j.micres.2018.11.009 Use first author et. al Antagonism Bacillus acidiceler Fusarium solani Briefly, each bacterial isolate (n = 45) was streaked to prepare a bacterial lawn onto a base plate containing LB medium (Chaurasia et al., 2005; Gao et al., 2017). Lids were removed and replaced by another base plate containing in its center a disc of 5 mm diameter of fungal mycelium on PDA. Both base plates were sealed with Parafilm and incubated for seven days at 30C. Each bacterial isolate was tested for antifungal activity in triplicate. Three assays were set up without bacterial treatments (LB only) and used as controls. Solid Biofilm batch culture aerobic avocado plant roots engineered Confocal laser scanning microscopy and scanning electron microscopy were used to calculate the percentage of mycelia growth inhibition (by coomparing the diameter of fungal mycelial growth in the control versus when the fungus was allowed to interact with the bacteria spp.) Metabolic (bacterial volatile organic compounds known as VOC's such as ketone, pyrazines and sulfur-containing compounds were found to reduce mycelial growth in particular fungal species) no Patrick Lima Joan Donahue
Guevara-Avendao, E., Bejarano-Bolivar, A. A., Kiel-Martinez, A.-L., Ramirez-Vazquez, M., Mendez-Bravo, A., von Wobeser, E. A., Reverchon, F. (2019). Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides. Microbiological Research, 219, 74-83. https://doi.org/10.1016/j.micres.2018.11.009 Antagonism Bacillus mycoides Colletotrichum gloeosporioide Briefly, each bacterial isolate (n = 45) was streaked to prepare a bacterial lawn onto a base plate containing LB medium (Chaurasia et al., 2005; Gao et al., 2017). Lids were removed and replaced by another base plate containing in its center a disc of 5 mm diameter of fungal mycelium on PDA. Both base plates were sealed with Parafilm and incubated for seven days at 30C. Each bacterial isolate was tested for antifungal activity in triplicate. Three assays were set up without bacterial treatments (LB only) and used as controls. Solid Biofilm batch culture aerobic avocado plant roots engineered Confocal laser scanning microscopy and scanning electron microscopy were used to calculate the percentage of mycelia growth inhibition (by coomparing the diameter of fungal mycelial growth in the control versus when the fungus was allowed to interact with the bacteria spp.) Metabolic (bacterial volatile organic compounds known as VOC's such as ketone, pyrazines and sulfur-containing compounds were found to reduce mycelial growth in particular fungal species) no Patrick Lima Aidan Pavao
Guevara-Avendao, E., Bejarano-Bolivar, A. A., Kiel-Martinez, A.-L., Ramirez-Vazquez, M., Mendez-Bravo, A., von Wobeser, E. A., Reverchon, F. (2019). Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides. Microbiological Research, 219, 74-83. https://doi.org/10.1016/j.micres.2018.11.009 Antagonism Bacillus mycoides Fusarium solani Briefly, each bacterial isolate (n = 45) was streaked to prepare a bacterial lawn onto a base plate containing LB medium (Chaurasia et al., 2005; Gao et al., 2017). Lids were removed and replaced by another base plate containing in its center a disc of 5 mm diameter of fungal mycelium on PDA. Both base plates were sealed with Parafilm and incubated for seven days at 30C. Each bacterial isolate was tested for antifungal activity in triplicate. Three assays were set up without bacterial treatments (LB only) and used as controls. Solid Biofilm batch culture aerobic avocado plant roots engineered Confocal laser scanning microscopy and scanning electron microscopy were used to calculate the percentage of mycelia growth inhibition (by coomparing the diameter of fungal mycelial growth in the control versus when the fungus was allowed to interact with the bacteria spp.) Metabolic (bacterial volatile organic compounds known as VOC's such as ketone, pyrazines and sulfur-containing compounds were found to reduce mycelial growth in particular fungal species) no Patrick Lima Aidan Pavao
Shimoyama T, Kato S, Ishii S, Watanabe K. "Flagellum Mediates Symbiosis." Science 20 Mar 2009: Vol. 323, Issue 5921, pp. 1574 Syntrophy Pelotomaculum thermopropionicum Methanothermobacter thermautotrophicus Coculture cultivation was conducted at 55C under an atmosphere consisting of N2 plus CO2 (80:20, vol/vol) without shaking, in 50 mL of 0.1% Bacto yeast extract supplemented with ethanol. liquid planktonic batch culture anaerobic sewage sludge engineered Headspace gas routinely sampled from cultures to measure partial pressures of methane and hydrogen gas during culturing. Microarrays were used to evaluate effect of FilC and FilD on M. thermautotrophicus methanogenesis-related genes. Adhesion of bacterial P. thermopropionicum flagellum (specifically FilD) to archaeon M. thermoautotrophicus initiates syntropy by triggering upregulation of methanogenesis-related genes in the archaeon. yes Aidan Pavao
Pang, Zhili, et al. Competition Between Pyrimorph-Sensitive and Pyrimorph-Resistant Isolates OfPhytophthora Capsici. Phytopathology, vol. 104, no. 3, 2014, pp. 269-274., doi:10.1094/phyto-07-13-0185-r. Competition Pyrimorph-Resistant Isolate of Phytophthora capsici Pyrimorph-Sensitive Isolate of Phytophthora capsici Mixed zoorospore suspensions of both resistant and sensitive isolates were placed in a carrot agar in vitro test Solid Agar Media Biofilm PDA Plates, continuous culture Aerobic The filamentanous oomycete pathogen Phytophthora capsici is an oomycete plant pathogen first recovered from chili plants. It can be found in a wide range of host environments including solanaceous plants, snap and lima beans, and cucurbits. Natural In terms of in vitro competition, the pyrimorph-resistant isolates were less fit than the pyrimorph-sensitive isolates. In terms of competitive ability in planta, the same results were observed. Resource Competition No Mary Brouder Sophia Al-Shwauva
Meng, X., Wu, Q., Wang, L. et al. J Ind Microbiol Biotechnol (2015) 42: 1601. https://doi.org/10.1007/s10295-015-1647-0 Inhibitory interactions, and metabolism stimulating. Saccharomyces cerevisiae Bacillus licheniformis Single cultures of S. cerevisiae and B. licheniformis and mixed cultures of varying inocculation ratios in YPD liquid medium at 30 degrees C and LB liquid medium at 37 degrees C. Liquid Medium Biofilm Continuous culture Aerobic S. cerevisiae is a yeast found naturally on the skin of fruits. B. licheniformis is a bacterium commonly found in soil. Engineered By providing a mixed culture of S.cerevisiae and B.licheniformis, flavor metabolism was greatly improved for Chinese Maotai flavor liquor making. S.cerevisiae had an inhibitory effect on B.licheniformis, while B.licheniformis increased the metabolic activity of S. cerevisiae. Metabolic No Mary Brouder Declan Ryan
Alexandra L. McCully, Megan G. Behringer, Jennifer R. Gliessman, Evgeny V. Pilipenko, Jeffrey L. Mazny, Michael Lynch, D. Allan Drummond, James B. McKinlay. Appl. Environ. Microbiol. Jul 2018, 84 (14) e00404-18; DOI: 10.1128/AEM.00404-18 Mutualistic CoExistence Eschericia coli Rhodopseudomonas palustris A coculture of fermentative Eschericia coli and phototrophic Rhodopseudomonas palustris Solid Biofilm A continuous coculture (required carbon and nitrogen supplied) Basal Anaerobic Minimal Medium E. coli is found in the intestines of warm blooded animals, and R. palustris is found commonly in lagoons, ponds, and marine sediments. Engineered By genetically disrupting E. coli transcriptional regulator NtrC, the researchers discovered that a nitrogen starvation response is key for a stable coexistence between EColi and R.palustris. In the coculture, E. coli and R. palustris perform complementary anaerobic metabolic processes, and the products of these reactions serve as key nutrients for the other microbe. For example, E. coli ferments glucose into acetate, lactate, and succinate (the carbon sources for R. palustris). Additionally, transcription levels via RNA-seq and proteomics were utilized to establish differences in levels of transcript and proteins in cocultures and monocultures. Metabolic No Mary Brouder Declan Ryan
Molina-Santiago, C. , Udaondo, Z. , Cordero, B. F. and Ramos, J. L. (2017), Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli. Environmental Microbiology Reports, 9: 441-448. doi:10.1111/1758-2229.12553 Cross Talk, Competition for Resources Eschericia coli Pseudomonas putida (Specifically, P. putida DOT?T1E, a strain isolated from a wastewater treatment plant in Granada, Spain Monocultures and A coculture of the two species at 30 degrees C in LB liquid medium, chosen as the growth medium because both strains grow at similar rates in it. Liquid Medium Biofilm Continuous culture Aerobic Both are microbes found commonly on the surface of vegetables, in freshwater and in waste water Engineered The two microbes, which occupy similar niches in nature, are able to adapt and defend themselves against each other. When cultured together, the species are able to alter their transcriptional profiles, particularly for central carbon metabolism, adhesion to surfaces, and the activation of drug efflux pumps. EColi was found to begin producing acetate in response to Pseudomonas putida. Resource Competition No Mary Brouder Jude Aboukhater
Alexandra L. McCully, Megan G. Behringer, Jennifer R. Gliessman, Evgeny V. Pilipenko, Jeffrey L.Mazny, Michael Lynch, D. Allan Drummond, James B. McKinlay (doi: 10.1038/s41598-018-38253-4) Antagonism Lactobacilli species: L. jensenii (LJ2 and 5), ?L. mucosae (LM2), and L. gasseri (LG1) Gardnerella Vaginalis Lactobacillus culutred in MRS broth for 24 hours, standardized, incubated for an additional 48 hours and filtured with 0.2??m cellulose acetate filters. G vaginalis cultures grown in brain heart infusion broth at 37 C for 48 hours and subsequently incubated with Lactobacillus supernatant for 24 hours at 37 C. Absorbance taken of liquid cultures. Liquid cultures plated on brain heart infusion medium for 24 hours at 37 C. liquid and then solid medium planktonic, and then biofilm continuous culture anaerobic Vaginal Tract natural Interaction identified through measuring the optical density at 600 nm of cultures of G. Vaginalis incubated with Lactobacillus compared to the optical density at 600 nm of cultures of G. Vaginalis without Lactobacillus incubation. Metabolic - the hydrogen peroxicde produced by Lactobacillus acidified culture medium and inhibitied G. vaginalis growth. no Used in studies to treat bacterial vaginosis. Sophia Al-Shwauva Jude Aboukhater
Appl. Environ. Microbiol. Jul 2018, 84 (14) e00404-18; DOI: 10.1128/AEM.00404-18 mutualism/prey-predation Eschericia coli Acanthamoeba castellanii A. castellanii cultured in PYG media, incubated at 30 C. A rifampicin-resistant strain of E. coli was isolated from the cerebrospinal fluid of a neonate affected by meningitis. All E. coli specimen were cultured in a Luria-Bertani broth overnight. . Liquid/Solid Planktonic for isolation/biofilm for association batch aerobic cerebrospinal fluid Natural The interactions were characerized on three separate assays, one for association, invasion, and cell survival. The association assay used a PYG media. The invasion and surival assays used the same media but included the addition of gentamicin. The association assay analyzed general interactions between E. coli and A. castellanii, the invasion assay analyzed the ability of E. coli to invade or be taken up by A. castellanii, and the survival assay analyzed the interactions between the two over a long period of time. Both invasive and non-invasive strains of E. coli were used.The E. coli colonies were counted for all three assays Invasive strains of E. coli are taken up more by A. castellanii than the non-invasive strain. The invasive strains also survive intracellularly when taken up by A. castellanii, bu the non-invasive strain did not. A. castellanii acts as a host for pathogenic bacteria like E. coli and helps them spread easily into and throughout the human body no Daniel Garvey Maya Coley
Schlecht LM, Peters BM, Krom BP, et al. Systemic Staphylococcus aureus infection mediated by Candida albicans hyphal invasion of mucosal tissue. Microbiology. 2015;161(Pt 1):168-181. commensalism Staphylococcus aureus Candida albicans Dual-species biofilm of S. aureus cells adhered to C. albicans hyphae, in RPMI 1640 (with HEPES and L-glutamine), incubated at 37C for 1h with shaking. Also, real-time adhesion analysis with S.aureus culture flowed over C. albicans hyphae. Also, murine model of oral infection: mice (immunosuppressed with cortisone acetate, oral microbiota suppressed with ampicillin) were exposed to C. albicans and S. aureus cultures on the tongue and continually exposed to C. albicans through drinking water. solid Biofilm batch aerobic oral natural Adhesion assays analyzed under light microscope to evaluate ability of S. aureus strains to attach to C. albicans (WT or ?Als3p). PNA-FISH staining and confocal scanning laser microscopy were used to analyze biofilm structure. Tongue histopathology on murine model and scanning confocal laser microscopy was used to evaluate co-penetration of tissue in immunosuppressed subjects with S. aureus and C. albicans. Data analysis was performed using the two-tailed Student's t-test, the Log Rank Test, or the Mann-Whitney U Test (two tailed), where appropriate S. aureus cells adhere to C. albicans hyphae by binding to the fungal adhesin Als3p in vitro, as illustrated using static and time lapse microscopy and then this allows them to penetrate host tissue and results in a synergistic infection, even when an infection would not be observed in the two strains alone. No Aidan Pavao Jude Aboukhater
"Mounier, J., Monnet, C., Vallaeys, T., Arditi, R., Sarthou, A.-S., Helias, A., & Irlinger, F. (2007). Microbial Interactions within a Cheese Microbial Community. Applied and Environmental Microbiology, 74(1), 172-181. https://doi.org/10.1128/aem.01338-07 Competition or Antagonism (unclear) Yarrowia lipolytica Debaryomyces hanseni 9 microbe strains used to create a model microbiome in order to make cheeses to be used in the experiment. Cultures originally isolated from Livarot cheese. The cheeses were sampled every 21 days for analysis of microbe growth. 1g samples of cheese were homogenized and diluted (1:10 w/ NaCL). Bacteria was removed from the yeast by plating on BHI agar with 50 g/L of amphotericin for 5 days at 25 C. Yeast-glucose-chloramphenicol agar was supplemented with 0.01 g/liter tetrazolium chloride after three days of incubation at 25 C for isolation of yeast. Solid biofilm batch aerobic cheese natural Counts of different yeast strains taken directly from counting colonies on solid media from the method described under "characterization environment." Comparison of colony populations used statistical variance analysis, and differences were furthmore analyzed using Student-Newman-Keuls test. Growth of another yeast resulted in competition for nutrients or negative interactions that resulted in lesser growth of D. Hanseii in its stationary growth phase. The exact mechanism unclear. No Effect not pronounced. Sophia Al-Shwauva Patrick Lima
"Mounier, J., Monnet, C., Vallaeys, T., Arditi, R., Sarthou, A.-S., Helias, A., & Irlinger, F. (2007). Microbial Interactions within a Cheese Microbial Community. Applied and Environmental Microbiology, 74(1), 172-181. https://doi.org/10.1128/aem.01338-07." Commensalism Luecobacter Geotrichum candidum 9 microbe strains used to create a model microbiome in order to make cheeses to be used in the experiment. Cultures originally isolated from Livarot cheese. The cheeses were sampled every 21 days for analysis of microbe growth. 1g samples of cheese were homogenized and diluted (1:10 w/ NaCL). Bacteria was removed from the yeast by plating on BHI agar with 50 g/L of amphotericin for 5 days at 25 C. Yeast-glucose-chloramphenicol agar was supplemented with 0.01 g/liter tetrazolium chloride after three days of incubation at 25 C for isolation of yeast. solid biofilm batch aerobic cheese Natural (but engineered cheeses in some cases to isolate specific interactions to be studied independent of other microbes) Count for bacteria population involved isolating 250 colonies of each cheese sample at random with sterile toothpicks and transfering the samples onto 96 well microtiter plates with BHI brothsupplemented with 10% glycerol and incubated for 3 days at 25 C. Comparison of colony populations used statistical variance analysis, and differences were furthmore analyzed using Student-Newman-Keuls test. Growth of Luecobacter was seen only in the cheeses containing G. candidum, suggesting G. candidum provides necessary supplementation for the growth of luecobacter. Possibly, G. candidum deacidfied the cheese environment (ideal for Luecobacter) or its metabolic products promoted Luecobacter growth. no Sophia Al-Shwauva Patrick Lima
Molecular and chemical dialogues in bacteria-protozoa interaction Chunxu Song, Mark Mazzola, Xu Cheng, Janina Oetjen, Theodore Alexandrov, Pieter Dorrestein, Jeramie Watrous, Menno van der Voort, Jos M. Raaijmakers prey-predation Pseudomonas fluorescens Naegleria americana P. fluorescens was grown Difco plates and in liquid King's media. N. americana was propogated via cultivation using heat-killed E. coli as a food source. solid biofilm in situ aerobic soil natural Precultured P. fluorescens was streaked across a nutrient broth extract agar (NBY) at a width of 4 mm. The bacteria were incubated for 3 hours at 25 C. A suspension of N. americana was spot-inoculated at one end of the bacterial growth. Incubation again for 3 days at 25 C. The P. fluorescens were counted at the end of the incubation period. Gene expression: when in presence of N. americana, P. fluorescens exhbitied altered gene expression no Daniel Garvey Declan Ryan
Li X, Hoogenkamp MA, Crielaard W, Deng DM. Diversity of Streptococcus mutans strains in bacterial interspecies interactions. J Basic Microbiol. 2014 Feb; 54(2): 97-103 https://doi.org/10.1002/jobm.201200457 competition Streptococcus mutans Enterococcus faecalis S. mutans biofilms grown in 96-well plate on polystyrene pegs 24h, which are then transfered to a 96-well plate containing E. faecalis suspension for 8h, then incubated in sterile BM for 16h. Biofilms then treated with CHX to evaluate antibiotic resistance. solid biofilm batch aerobic oral/dental natural Biofilm formation evaluated with biomass staining assay, reazurin, viable count and competition assay. Dual-species biofilm formation decreased with presence of E. faecalis. Biofilm formation and antibiotic resistance are dependent on the strain of S. mutans. S. mutans and E. faecalis are thought to inhibit each other's growth through bacteriocins. no Aidan Pavao Joan Donahue
Genre, Andrea et al. Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection Plant cell vol. 17,12 (2005): 3489-99. symbiotic Medicago truncatula Gigaspora gigantea Transformed root cultures from M. truncatula and two mutants were incoulated with G. giganta in vivo and observed with a microscope. solid biofilm insitu aerobic plant roots engineered (modified strains) Hyphal contact was monitored with a stereomicroscope and and potentail infection points were observed with a confocal microscope. A laser band of 488 nm excited G. giganta autoflorescence. The mutants are unable to create the prepenetration apparatus, and the Gigaspora could not colonize any of the mutants after penetration, so the mutations decrease the possibility of penetration events no Claire McCann Jien Li
syntrophic Geobacter sulfurreducens PCA Desulfotomaculum reducens MI?1 Co-cultures were established with a modified Widdel-based medium; with either Fe(III)-citrate and Fe(III)-oxide defined media. Cultures were incubated at 30 degrees Celsius. Black biofilm formed after 1-2 days of incubation and after ~100 hr, completely sticked to the culture vessels. insoluble Fe(III)-oxide media, soluble Fe(III)-citrate media biofilm batch anaerobic anaerobic environments with heavy iron content (e.g. ocean sediment, deep underground) engineered (modified strains) Biofilm formation with acridine orange staining and fluorescent microscopy and gas chromatography (to measure hydrogen gas levels). G. sulfurreducens utilizes pyruvate-oxidation products -- acetate, hydrogen-- produced by D. reducens as electron donors to reduce Fe(III) to Fe(II). no Justin Nguyen Jien Li
amensalism and commensalism Streptococcus mitis or Streptococcus sanguinis Candida albicans C. albicans in Sabouraud dextrose agar and incubated at 37 degree Celsius for 24 hr. S. mitis and S. sanguinis in mitis salivarius agar (with 15% sucrose) incubated at 37 degree Celsius in 5% CO2. For the biofilm formation, a 97 well microtiter plate was used. 100 microliters of C. albicans inoculated with YNB (glucose 100 mM and 100 microliters). The plate was incubated again at 37 degree Celsius for 90 minutes for initial adhesion. Afterwards, each well was washed twice with 0.85% NaCl solution to then put 100 microliters of fetal bovine serum and two more hours of incubation. Biofilms of C. albicans with S. mitis and S. sanguinis in each specified well was inoculated with 50 microliters of streptococci standard suspension and glucose at a concentration of 100 mmol/L and 60 microliters of tryptic soy broth. Incubated for 48 hr at 37 degree Celsius in 5% CO2 (broth was changed after 24 hr). liquid biofilm batch; however, there were several addition of addtion of nutrients per incubation not specified (most likely oxygen) oral cavity (teeth and oral mucosal sufaces) natural After 48 hours, each well was washed with 0.85% NaCl solution, dispersed with ultrasonic homogenizer (50W for 30 seconds) and then transferred to Sabouraud dextrose agar plates (50 mg/L chloramphenicol. Incubated at 37 degree for another 48 hours. Colonies are counted to determine colony-forming unit (CFU). 1 mL of distilled water with 0% fetal bovine serum and 100 microliters of C. albicans standardized suspension to 24 well cell-culture plate. Then pipetted with 100 microliters of either S. mitis or S. sanguinis. After incubated at 37 degree Celsius for 24 hour, 50 microliter of each well spread on glass slide and analyzed under light microscope at x 400 magnification. Ten microscopic fields per slide to quantify C. albicans Filamentation. S. mitis inhibits filamentation, resulting in over-expression of specific genes and increase in virulence factor; while S. sanguinis increases filamentation, resulting in lower virulence. no Justin Nguyen Sophia Al-Shwauva
syntrophic photosynthesis Geobacter sulfurreducens Prosthecochloris aestuarii G. sulfurreducens PCA cultured routinely in nutrient broth medium with acetate and fumarate while P. aestuarii in a modified medium with 3.5 mM sodium sulfide (under LED light). Both grown at 30 degrees. Set up in two-chamber photosynthetic microbial fuel cell with the electrolytes as modified media. Purce cultures were washed three times with anaerobic anolyte/catholyte and put into the chambers. The anodic chamber (containing G. sulfurreducens) was enwrapped with aluminum foil to maintain complete darkness. Cathodic chamber lit up by LED light. All of this proceeds at 30 degree Celsius in batch. liquid culture biofilm batch with the photosynthetic microbial fuel cells; in situ with electrochemical FTIR spectroscopy anaerobic anaerobic environments (e.g. soil and aquatic sediments) natural? Cell voltages were recorded every two minutes by an electrochemical data measurement system. The anode/cathode biofilms were stained to be analyzed under a confocal laser scanning microscope. Further confirmed with FTIR in situ spectroscopy with sample potententisl at -800 to 200 mV with interval of 200 mV. G. sulfurreducens oxidize acetate (anode compartment, transferring the electrons across with an external metal wire) where the electrons are utilized by P. aestuarii to perform photosynthesis. no Justin Nguyen Jien Li
inhibitory regulation/ amensalism Pseudomonas piscium Fusarium graminearum Wheat heat samples at 50%/100% flowering done with dilution plating for cultural bacterial isolation. Five samples were selected and homogenized with a sterilized mortar and pestle. Then serially diluted in sterile 0.85% NaCl solution and then plated on LB agar plates (with fungicide carbendazim). Incubated at 25, 30, 37 degree Celsius for 1-3 days. Tested in triplicate with inhibition zones measured after 5 days of co-culture at 25 degree Celsius. co-culture; solid biofilm in situ happened with the microbiome sequencing and analysis; however, to analyze the interaction, it was using the wheat heads onto agar plates with batch method. not specified plant microbiome/ rhizosphere natural Western blot analysis to detect histon acetylation and gene expression of wild-type strain. Biofilm formation and biocontrol experiments done both in growth chamber and in the field: Mid-anthesis stage wehat heads grown in the chamber sprayed with biocontrol strain ZJU60 of Pseudomonas piscium using atomizer. After preventive treatments for 6 hours, each wheat head sprayed with 3 ml of Fg strain PH-1 and imaged after incubation for 7 days (25 weat heads each experiment; repeated twice). Then gas chromatography cellular fatty acid analysis and high-throughput matrix-assisted laser desorption/ionization system. Pseudomonas piscium secretes phenazine-1-carboxamide that affects fungal protein (FgGcn5), causing deregulation of histon acetylation in F. graminearum that results in inhibiting fungal growth/virulence and mycotoxin biosynthesis. P. piscium ZJU60 secreted PCN metabolites to inhibit Fusarium graminearum (Fg) growth. no Justin Nguyen Daniel Garvey
Rodriquez-Verdugo A, Vulin C, Ackermann A. The rate of enviormental fluctuations shapes ecological dynamics in a two species microbial sysyem. Ecol Lett. 2019 Feb 21. doi: 10.1111/ele.13241. competition & commensalism Acinetobacter johnsonii Pseudomonas putida After 24 h of bacterial growth, 1% of the population was diluted in fresh medium. This was done with both mono and co-cultures for 6 days. Batch cultures were grown in 40 mL glass vials with screw caps. Vials were submerged overnight in 0.2 N HCl and rinsed twice with deionised water. Vials were also heated in a Muffle oven to 500C for 3 h. Screw caps were soaked in a 10% sodium persulphate solution at 60C for 1 h, rinsed twice with deionised water and air?dried. Single colonies were grown in LB broth and supplemented with antibiotics. Cultures were incubated overnight at 30C with constant shaking (220 rpm). liquid culture; both mono and co-cultures planktonic cells continuous culture aerobic A. johnsonii is native to sewage and freshwater habitats. P. Putida naturally occurs in soil and water exposed to oxygen. The A. johnsonii strain occured naturally and the P. putida strain was engineered. Cells were washed and diluted into fresh AB medium supplemented with the desired carbon source. Cells were incubated for 1 day at 30C and shaken. Cultures were then again diluted in fresh AB medium with appropriate carbon source for both mono and co-cultures. Cultures underwent daily transfers into fresh medium for 6 days. Each day, population densities of A. johnsonii and P. putida were estimated by plating on LB agar. The identification method was co-occurence. An estimate for the slope of the linear regression for each interaction was generated based on time and the log10 of the densities estimated at the end of each 24 h growth cycle. The population densities were compared over the 6 days for each species in both monocultures and co?cultures. A a t?test was performed over the means. resource competition; Interspecies interactions change depending on the carbon source provided. Yes. https://doi.org/10.5061/dryad.734q42p Katelyn Davidson Jien Li
C. Kampmann et al. Composition of human faecal microbiota in resistance to Campylobacter infection. Bacteriology. Volume 22, Issue 1. January 2016. Colonization resistance Campylobacter jejuni Lachnospiraceae coprococcus Stool samples were collected from volunteers before and after travel. One sample was used for DNA extraction/analysis, the other was used to culture C. jejuni for ease of idenitificaiton of infection. C. jejuni was cultured on modified charcoal cefoperazone deoxycholate agar plates. solid Not specified batch culture anaerobic human gut natural Two stool samples were taken from healthy swedish adults before and after travel to countries with reasonable risk of infection by a bacterial enteropathogen. One sample was used for routine culturing, the other for DNA extraction. DNA extraction and identification of species was used by amplifying the 16 S region of the genome. In those uninfected and those infected with C. jejuni, levels of L. Coprococcus was statistically analyzed. unknown no Largely a culture-independent study, only C. jejuni was cultured. The rest of the experiment was achieved through DNA analysis. Joan Donahue
Simo G, Kante ST, Madinga J, Kame G, Farikou O, llombe G, Geiger A, Lutumba P, Njiokou F. Molecular identification of Wolbachia and Sodalis glossinidius in the midgut of Glossina fuscipes quanzensis from the Democratic Republic of Congo. Parasite. 2019;26:5. DOI: https://doi.org/10.1051/parasite/2019005 competition/mutal inhibition Sodalis glossinidius Wolbachia After Tsetse flies were collected and disected, the midgut of each fly was placed in a microtube containing 95 ethanol. Microtubes were initially kept at room temperature and then at 20C. The tissues were crushed with a pestle in CTAB buffer and incubated at 60C for 30 min. Tissues were supplemented with a chloroform/isoamylic alcohol mixture. liquid culture; well-mixed planktonic cells batch culture; DNA pellets were suspended in 30 ?L of sterile water anaerobic Both species are anaerobic and are commonly found in the midgut of various species of Tsetse flies. natural DNA was precipitated out by the addition of isopropanol (V/V) and centrifugation. The DNA pellets were then placed in sterile water and stored at 20C. The presence of S. glossinidius was determined by amplifying a specific DNA fragment with pSG2 primers. After PCR, products were analyzed by electrophoresis on agarose gel with ethidium bromide. Gels were visualized under UV light. Wolbachia was identified with primers pairs wsp F1 and wsp R. Products were alalyzed by electrophoreis and visualized under UV light. Five genes including gatB, coxA, hcpA, fbpA and ftsZ were analyzed in Wolbachia. Amplified fragments of fbpA from Wolbachia underwent sequencing. relatively unknown: Some antagonistic actions resulting from the biological effects of Wolbachia and S. glossinidius may occur in tsetse midgut during trypanosome infections. no Katelyn Davidson
Symbiosis insights through metagenomic analysis of a microbial consortium cooperation Olavius algarvensis O. algarvensis symbionts ?1, ?4, ?1 and ?3 fresh worms were removed from the sediment via decantation, cleaned by successive washes in sterile seawater and gently homogenized in 2 ml phosphate-buffered saline (PBS), pH 7.4 using a glass dounce homogenizer. A step gradient of 1.146-1.083 g/ml density was prepared with HistodenzTM (Sigma, St. Louis, MO) in 5 ml OpiSeal Polyallomer tubes (Beckman Coulter, Fullerton, CA) and the cell suspension loaded on top of the gradient. The overlain gradient was then centrifuged at 10,000 g in a Beckman L8-M ultracentrifuge and SW 55Ti swing rotor for 1 h at 4oC. Following centrifugation, 200-300 ?l fractions were withdrawn from the bottom of the gradient tube and diluted with 10 vol of PBS to remove excess nycodenz. Cells were pelleted and resuspended in PBS and fractions evaluated semi-quantitatively for the enrichment of bacterial cells using real-time PCR amplification of 16S and 18S rRNA genes. solid media (Original Sediment) Plankton in situ aerobic 5.6 m water depth in silicate sediments around sea grass beds of Posidonia oceanica in a bay off Capo di Sant' Andrea, Elba, Italy Natural Shotgun-sequencing and metagenomic data analysis Metabolic: In the O. algarvensis symbiosis, both reduced sulphur compounds and hydrogen can be used as energy sources, and all four symbionts have the potential to fix CO2 into organic carbon via autotrophy. In addition, the sulphate-reducing symbionts can feed the oligochaete host through heterotrophy by taking up dissolved organic carbon. No Jien Li Katelyn Davidson
Metabolic Commensalism and Competition in a Two-Species Microbial Consortium commensalism/competition Pseudomonas putidastrain R1 Acinetobacter strain C6 Strains were grown in FAB medium [1 mM MgCl2, 0.1 mM CaCl2, 0.01 mM Fe-EDTA (Sigma Chemical Co., St. Louis, Mo.), 0.15 mM (NH4)SO4, 0.33 mM Na2HPO4, 0.2 mM KH2PO4, and 0.5 mM NaCl] supplied, unless otherwise mentioned, with benzyl alcohol (Merck, Darmstadt, Germany) as the sole carbon source. When required, antibiotics were added at final concentrations of 100 ?g/ml for streptomycin, 50 ?g/ml for nalidixic acid, and 10 ?g/ml for kanamycin. solid and liquid media (mostly liquid) plankton and biofilm (competition in plankton, commensalism in biofilm) continuous culture aerobic most soil and water habitat where oxygen is available natural platting and Imaging Metabolic or resource competition No Jien Li Justin Nguyen
Species-species interactions modulate copper toxicity under different visible light conditions commensalism/mixed(depends on light condition) Chlamydomonas reinhardtii CPCC11 Synechocystis sp. PCC6803 Mono- and multialgal cultures acclimated to low-intensity light were exposed to Cuconcentrations and incubated under visible light of increasing intensity. liquid plankton modified BG11 medium containing NH4NO3 as N-source instead of NaNO3 and FeCl3 instead of ammonium iron citrate (Table S1). pH was maintained at 7.5 using 1 mM 3-(N-morpholino)propanesulfonic acid (MOPS, Sigma-Alrdich, Buchs, Switzerland). Microbes were grown under chemostat conditions with fresh media added every 48 hours. aerobic water and damp soil natural engineered flow cytometry Unknown Yes. https://ars.els-cdn.com/content/image/1-s2.0-S0147651318313241-mmc1.pdf Jien Li Ryan Oleynik
NOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES Cooperation Salmonella typhimurium LT2 E. coli K12 BW25113 with a metA knockout M9 minimal media with 10 mL of 0.01 M CaCl2, 10 mL of 0.1 M MgSO4, and 10 mL of 20% sugar (lactose or glucose) per liter solid and liquid media not specified (seems like biofilm) Since it isn't explicitly stated in the paper, it might be a good idea to use examples/evidence from paper to explain why you think it is biofilm. batch culture and continuous culture aerobic intestinal tracks and manure engineered methionine?excreting Salmonella was competed against nonexcreting wild?type in the presence of met?E. coli. Additionally, the effect of mass action was tested. the number of E. coli and Salmonella were determined by plating on LB plates with X?gal. To determine the frequency of excreters and nonexcreters, 30 Salmonella colonies were stabbed onto a lawn of E. coli on a lactose plate with X?gal. If an isolate was an excreter a blue colony formed on the plate, otherwise no colony appeared. metabolic No. Jien Li Mary Brouder
Xu, Z., Shao, J., Li, B., Yan, X., Shen, Q., & Zhang, R. (2013). Contribution of bacillomycin D in Bacillus amyloliquefaciens SQR9 to antifungal activity and biofilm formation. Applied and environmental microbiology, 79(3), 808-15. amensalism/antagonism Bacillus amyloliquefaciens SQR9 Fusarium oxysporum B. amyloliquefaciens SQR9 was grown in Landy medium at 30C for 60 h and the lipopeptides were isolated. F. oxysporum was grown for 5 days in PDA plate at 25C. A plug (about 1 cm in diameter) of F. oxysporum was placed in the center of plate and incubated at 25C. solid media; liquid media (well-mixed) biofilm batch culture Aerobic roots of cucumber plants Engineered Antifungal activity of B. amyloliquefaciens SQR9 was examined by Reversed-phase HPLC chromatograms. Antifungal compounds in B. amyloliquefaciens SQR9 were identified and analyzed by LC-MS. PDA plates used to measure growth inhibition of F. oxysporum by B. amyloliquefaciens SQR9: measured average distance between the edges of petri dish and the fungal mycelium. Biofilm formation by B. amyloliquefaciens was analyzed through Microtiter plate assay. Antibiotic: Bacillus amyloliquefaciens SQR9 produces lipopeptide compounds (bacillomycin D) that inhibits growth of Fusarium oxysporum. yes: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568560/ Seung Woo Kim Katelyn Davidson
Skekhawat K, Patterson H, Bauer FF, Setati ME. RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions. BMC Genomics. 2019. 20:145. https://doi.org/10.1186/s12864-019-5511-x competition Saccharomyces cerevisiae Lachancea thermotolerans Batch fermentations were carried out in synthetic grape juice medium Continuous in-flow and out-flow of the medium was implemented for single and mixed fermentations. Feeding medium contained both glucose and fructose. Strains were grown on solid media and fermentation ocuured in well mixed liquid media planktonic cells continuous culture Fermentations preformed under both anaerobic and aerobic conditions. Saccharomyces cerevisiae is commonly found in the skin of grapes. Similarly, Lachancea thermotolerans occurs in naturally fermented foods. Natural Both species were identified based on colony morphology on the plates. The concentrations of fructose, glucose, acetaldehyde and acetic acid were analyzed using enzymatic kits. Ethanol was measured by liquid chromatography. Volaties were analyzed by Gas Chromatography with Flame Ionization Detection. Cell samples for RNA-sequencing were obtained from both single and mixed culture fermentation. Concentration of RNA was determined by spectrophotometry. Annotation of genomic features was performed using the reference genomes of S. cerevisiae S288c and L. thermotolerans CBS6340. For the selection of differentially expressed genes statistical modelling was used. metabolic Yes. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112581 Katelyn Davidson Joan Donahue
Chew SC, Yam JKH,Matysik A, Seng ZJ, Klebensberger J, Givskov M, Doyle P, Rice SA, Yang L, Kjelleberg S. Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus. MBio. 2018 Nov 6;9(6). DOI: 10.1128/mBio.00585-18 competition and syntrophy P. aeruginosa S. aureus P. aeruginosa was grown in LB medium and S. aureus was grown in TSB medium, both at 37C with shaking. solid media; both mono and co-cultures were analyzed biofilm batch culture aerobic Pseudomonas aeruginosa and Staphylococcus aureus are commonly found in infections of cystic fibrosis (CF) lungs and in diabetic and chronic wounds. Staphylococcus aureus occurs naturally but Pseudomonas aeruginosa mutants were genetically engineered. Biofilms were visualized using a Zeiss LSM780 confocal scanning laser microscopy. P. aeruginosa strains were fluorescently marked using miniTn7-mCherry. S. aureus 15981 was fluorescently marked using pSB2019, expressing Gfp. Gfp was detected by argon laser for excitation. The biovolumes, microcolony sizes, and surface coverage values were analyzed with COMSTAT and logarithmic transformation of the data. Significant differences between the distributions of microcolony sizes were determined by the Kolmogorov-Smirnov test. Fluorescent latex beads were dispersed in TSB medium and movement was observed by fluorescence microscopy. Mono and co-culture biofilms were grown in 24-well plates for 19?hours. The cell pellets were plated on agar for CFU counting of P. aeruginosa cells. Cells from monospecies S. aureus biofilms were plated on TSB agar for CFU counting. Pyoverdine and Pseudomonas quinolone signal (PQS) assay were performed. metabolic/ resource competition: P. aeruginosa was found to compete with S. aureus for oxygen and induced the bacterium to shift to fermentative metabolism to produce lactate, which P. aeruginosa consumed. P. aeruginosa can also lyse S. aureus to obtain iron. No. Katelyn Davidson Justin Nguyen
Benoit-Gelber I, e. (2017). Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran. - PubMed - NCBI. competition (previously described as so) The authors cite research that found the relationship was competitive (background section), however their work indicates that there was no sign of competition (see conclusion section) OK Aspergillus niger Aspergillus oryzae Spores of A. niger and A. oryzae were isolated from complete medium plates containing 2% glucose. Liquid shaken cultures were inoculated and incubated for 16 h at 30C and 250 rpm in 1L Erlenmeyer flasks with 250 ml transformation medium (TM) or minimum medium with wheat bran 1%. solid culture then to liquid cultures for further use planktonic cells batch culture aerobic A. niger is found in decomposing plant materials but also grow on bathrooms and carpet dust. A. oryzae usually found in man made settings in oriental food fermentation engineered Flow cytometry, Light Microscopy, Quantitative Proteome Analysis, qPCR A. niger and A. oryzae secrete a broader range of plant cell degrading enzymes in mixed culture versus monoculture. yes: https://www.sciencedirect.com/science/article/pii/S1087184517300257#s0045 Seung Woo Kim Ryan Oleynik
Neupane, S., Finlay, R., Alstrom, S., Elfstrand, M. and Hogberg, N. (2014). Transcriptional responses of the bacterial antagonist Serratia plymuthicato the fungal phytopathogen Rhizoctonia solani. Wiley Online Library. antibiosis/amensalism R. solani S. plymuthica AS13 A dual culture assay of bacteria and fungus was carried in agar plates for 48 hours after which the bacteria was harvested for analysis. solid media; co-culture biofilm batch culture aerobic oilseed rape engineered Plating/Bacterial RNA?seq analysis S. plymuthica AS13 increases expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters (major facilitator superfamily and PTS systems). S. plymuthica AS13 also protected against oxidative damage. yes: https://onlinelibrary.wiley.com/doi/full/10.1111/1758-2229.12203 Seung Woo Kim Ryan Oleynik
Kastman, E. K., Kamelamela, N., Norville, J. W., Cosetta, C. M., Dutton, R. J., & Wolfe, B. E. (2016). Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species. mBio, 7(5), e01157-16. doi:10.1128/mBio.01157-16 commensalism S. equorum Scopulariopsis S. equorum was isolated from cheese rinds by serially diluting rind scrapings or milk samples on plate count agar with milk and salt with cycloheximide. Scopulariopsis was grown above static liquid cheese curd (2% cheese curd) for 2 weeks at 24C to obtain fungal supernatants. Solid media (cheese curd agar plates) biofilm in situ and batch culture aerobic cheese rind biofilms Natural for sequencing, engineered for CCA plates Whole-genome shotgun metagenomic sequencing and optical density assays (using SpectraMax M5 plate reader). For each metagenome sequenced, a 5.2 million base pair section was mapped against a reference genome and % relative abundance was calculated for each species. The niches of three Staphylococcus species was examined by growth in different salt and pH conditions, followed by optical density. OK Scopulariopsis potentially allows S. equorum to dominate in communities through complex iron utilization pathways. no Seung Woo Kim Mary Brouder
D'Onofrio, Anthony et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry & biology vol. 17,3 (2010): 254-64. commensalism and Interspecies symbiosis Maribacter polysiphoniae KLE1104 Micrococcus luteus KLE1011 The two strains, suspended from saind biofilms, were streaked on half of a R2sea plate and subsequently cross streaked resulting in regions of proximal, distal and overlapping inoculation. The uncultured isolates were found by their decreasing growth with increasing distance from the cultured helper strain on the cross streak plates. solid media biofilm batch culture aerobic Sand grains natural Isolation spread plate of helper organism cross streaked with unculturable organism. The unculturable strain M. polysiphonae grew larger colonies when closer to the helper colonies on the streak plate. yes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895992/figure/F2/ Sophia Al-Shwauva Mary Brouder
Pseudomonas aeruginosa Promotes Escherichia coli Biofilm Formation in Nutrient-Limited Medium PLoS One. 2014; 9(9): e107186. Published online 2014 Sep 8. doi: 10.1371/journal.pone.0107186 Mixed (biofilm formation substantially modifies inter-species competitionand growth rates) Pseudomonas aeruginosa Escherichia coli Mono- and mixed-culture biofilm experiments were run using R2A media at room temperature (24C). These experiments were also conducted using 4x and 8x concentrated R2A medium in microfluidic flow cells to investigate the effects of nutritional conditions on growth of biofilm co-cultures. well-mixed biofilm batch culture aerobic Aquatic environments. E. coli and other enteric organisms can persist and potentially grow in drinking water distribution networks engineered Biofilm growth was observed using a 2-D planar flow cell, and a single-channel microfluidic flow cell [20] E. coli formed sparse biofilms composed of small, isolated cell clusters (grid unit is 23.8 um). B) Mixed P. aeruginosa and E. coli biofilm on day 6, after 3 days of mono-species E. coli growth plus 3 additional days of multi-species growth after inoculation of P. aeruginosa. (grid unit in B is 23.8 um). Following introduction of P. aeruginosa, E. coli grew prolifically and adopted a configuration similar to that observed in other mixed-species experiments. No Jude Aboukhater Sophia Al-Shwauva
Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation doi: 10.1128/mBio.01286-14 cooperation /mixed Staphylococcus aureus Propionibacterium acnes Staphylococcus spp. were grown aerobically using tryptic soy broth (TSB); Corynebacterium spp. were grown aerobically using brain heart infusion (BHI) with 1% Tween 80 (BHIT); Propionibacterium spp. were grown anaerobically using BHI. Complex media were BD brand (Becton, Dickinson, and Co.). Low-iron medium (SSD0Fe) used to grow S. aureus for aggregation and biofilm assays was prepared using published recipes (50, 51) as detailed in Text S1 in the supplemental material. Routine culture of antibiotic-requiring strains was with 10 ug/ml erythromycin. mixed, solid media biofilm batch culture aerobic nostril microbiota (Staphylococcus aureus resides primarily in human nostrils and colonizes at least a quarter of the U.S. population). pH range (4.5 to 6.5) Strains weren't engineered. Interaction naturally occurs in nostrils. Interaction on media was engineered To identify the small molecule(s) that induced S. aureus aggregation, we fractionated the crude P. acnes KPA171202 CM extract by preparative high-performance liquid chromatography (HPLC). The addition of P. acnes KPA171202 CM extract resulted in aggregation of both strains, yielding a significantly lower aggregation ratio (after 390 min) than that of a DMF-only control (Fig. 2A; two-tailed, paired t test, P < 0.001). (Aggregation ratio is the optical density at 600 nm [OD600] of a standing liquid culture at a given time posttreatment addition divided by the original OD600 of that culture immediately before treatment addition [t = 0]). These data indicate that P. acnes KPA171202 secretes into the environment an active principle that induces S. aureus aggregation. No Jude Aboukhater Katelyn Davidson
doi: 10.3389/fcimb.2017.00106. eCollection 2017. In vivo and In vitro Interactions between Pseudomonas aeruginosa and Staphylococcus spp. Hotterbeekx A1, Kumar-Singh S1,2, Goossens H1, Malhotra-Kumar S1. competition and counter-inhibition (co-colonization with the presence of certain environmental factors such as antibiotics) Staphylococcus aureus Pseudomonas aeruginosa In vivo and In vitro mixed biofilm and Planktonic In vivo as well as in vitro studies were referenced in this article to study the microbial interaction. aerobically environment-specific interactions occur in places like in the cystic fibrosis lung or in wound infections natural N/A (Multiple studies were referenced. Although the interaction between the species is described precisely, not one identification method is explained in this article) P. aeruginosa produces a wide variety of molecules that inhibit S. aureus in vitro P. aeruginosa strongly reduces or completely outcompetes S. aureus during co-culture in many in vitro model systems, both planktonic and biofilm (Palmer et al., 2005; Baldan et al., 2014; DeLeon et al., 2014). This anti-staphylococcal activity of P. aeruginosa was first described by Lightbown and Jackson (1956), who identified 4-hydroxy-2-heptylquinoline N-oxide (HQNO) as a major compound produced by P. aeruginosa that inhibited the cytochrome systems of some bacteria, including S. aureus. To be more specific: Extracellular factors produced by P. aeruginosa affect biofilm formation, oxidative respiration, cell lysis and virulence of S. aureus. Lysis of S. aureus leads to increased extracellular iron and N-acetyl glucosamine (GlcNac), which are sensed by P. aeruginosa. AHL, N-acyl homoserine lactone; HQNO, 4-hydroxy-2-heptylquinoline N-oxide; PQS, Pseudomonas quinolone signal; GlcNac, N-acetyl glucosamine. no Jude Aboukhater Mary Brouder
Majzoub ME, McElroy K, Maczka M, Thomas T, Egan S. Causes and Consequences of a Variant Strain of Phaeobacter inhibens With Reduced Competition. Front Microbiol. 2018;9:2601. Published 2018 Nov 2. doi:10.3389/fmicb.2018.02601 Competition Phaeobacter inhibens 2.10 Pseudoalteromonas tunicata Phaeobacter inhibens 2.10 WT (wild type) strain (Thole et al., 2012), P. inhibens NCV12a1 [non-inhibiting biofilm variant of P. inhibens obtained from (Lutz et al., 2016)], and P. tunicata D2 (Holmstrom et al., 1998) were routinely cultured in complex Marine Broth (Difco 2216 marine broth 37.4 g l?1) or Marine Agar (MA) (marine broth with 1.5% (w/v) Oxoid bacteriological agar). Bacterial strains were grown at 25C with constant agitation of broth cultures at a speed of 180 rpm. For long-term storage each bacterial strain was kept at -80C in 20% glycerol. liquid (broth); well mixed biofilm Continuous Culture Flow Cell System Biofilms aerobic marine surfaces natural co- occurance During biofilm dispersal P. inhibens 2.10 produces heritable phenotypic variants, including those that have a reduced ability to inhibit the co-occurring bacterium Pseudoalteromonas tunicata. yes; pictures included in the article Audrey Steely Justin Nguyen
Rakoff-Nahoum, S., Foster, K. R., & Comstock, L. E. (2016). The evolution of cooperation within the gut microbiota. Nature, 533(7602), 255-9. cooperation Bacteroides thetaiotaomicron Bacteroides ovatus in vitro solid biofilm batch and in situ in mice aerobic mammalian gut microbiota natural Plating Using in vitro systems and gnotobiotic mouse colonization models, we find that extracellular digestion of inulin increases the fitness of B.ovatusdue to reciprocal benefits when it feeds other gut species such as Bacteroides vulgatus yes; see images in article Audrey Steely Justin Nguyen
Fabio Cleisto Alda Dossi, Edney Pereira da Silva, and Fernando Luis Consoli, "Shifting the Balance: Heat Stress Challenges the Symbiotic Interactions of the Asian Citrus Psyllid, Diaphorina citri (Hemiptera, Liviidae)," The Biological Bulletin 235, no. 3 (December 2018): 195-203. mutual-symbiosis Diaphorina citri CandidatusCarsonella ruddii and Candidatus Profftella armatura in vitro solid biofilm batch and in situ aerobic plants engineered metabolic yes, see images Audrey Steely Katelyn Davidson

Acknowledgment: The work is supported by an Academic Technology Innovation Grant (ATIG) from Boston College. Database and website: Joy Zou. Content contributed by: Kyle Wiant, Nick Favazza, and students in 2018 and 2019 Microbiology classes at Boston College Department of Biology (BIOL4140).

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