The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity

Nai C, Meyer V. From axenic to mixed cultures: technological advances accelerating a paradigm shift in microbiology. Trends Microbiol. 2018;26:538–54.

PubMed  Google Scholar 

Powers MJ, Sanabria-Valentín E, Bowers AA, Shank EA. Inhibition of cell differentiation in Bacillus subtilis by Pseudomonas protegens. J Bacteriol. 2015;197:2129–38.

PubMed  PubMed Central  Google Scholar 

Sztajer H, Szafranski SP, Tomasch J, Reck M, Nimtz M, Rohde M, et al. Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans. ISME J. 2014;8:2256–71.

PubMed  PubMed Central  Google Scholar 

Trejo-Hernández A, Andrade-Domínguez A, Hernández M, Encarnación S. Interspecies competition triggers virulence and mutability in Candida albicans–Pseudomonas aeruginosa mixed biofilms. ISME J. 2014;8:1974–88.

PubMed  PubMed Central  Google Scholar 

Garbeva P, Silby MW, Raaijmakers JM, Levy SB, de Boer W. Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME J. 2011;5:973–85.

PubMed  PubMed Central  Google Scholar 

Yoshida S, Ogawa N, Fujii T, Tsushima S. Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium of Burkholderia sp. NK8 and Pseudomonas aeruginosa PAO1. J Appl Microbiol. 2009;106:790–800.

PubMed  Google Scholar 

Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Markillie LM, et al. Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing. ISME J. 2014;8:2243–55.

PubMed  PubMed Central  Google Scholar 

Ren D, Madsen JS, Sørensen SJ, Burmølle M. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation. ISME J. 2015;9:81–9.

PubMed  Google Scholar 

Al-Shabib NA, Husain FM, Ahmad I, Khan MS, Khan RA, Khan JM. Rutin inhibits mono and multi-species biofilm formation by foodborne drug resistant Escherichia coli and Staphylococcus aureus. Food Control. 2017;79:325–32.

Google Scholar 

Liu W, Jacquiod S, Brejnrod A, Russel J, Burmølle M, Sørensen SJ. Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. ISME J. 2019;13:3054–66.

PubMed  Google Scholar 

Li M, Wei Z, Wang J, Jousset A, Friman VP, Xu Y, et al. Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett. 2019;22:149–58.

PubMed  Google Scholar 

Goyal A, Dubinkina V, Maslov S. Multiple stable states in microbial communities explained by the stable marriage problem. ISME J. 2018;12:2823–34.

PubMed  PubMed Central  Google Scholar 

Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470–80.

PubMed  Google Scholar 

Faust K. Microbial consortium design benefits from metabolic modeling. Trends Biotechnol. 2019;37:123–5.

PubMed  Google Scholar 

Liang J, Bai Y, Men Y, Qu J. Microbe–microbe interactions trigger Mn(II)-oxidizing gene expression. ISME J. 2017;11:67–77.

PubMed  Google Scholar 

Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, et al. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. ISME J. 2019;13:494–508.

PubMed  Google Scholar 

Kong W, Meldgin DR, Collins JJ, Lu T. Designing microbial consortia with defined social interactions. Nat Chem Biol. 2018;14:821–9.

PubMed  Google Scholar 

Kelvin Lee KW, Hoong Yam JK, Mukherjee M, Periasamy S, Steinberg PD, Kjelleberg S, et al. Interspecific diversity reduces and functionally substitutes for intraspecific variation in biofilm communities. ISME J. 2016;10:846–57.

PubMed  Google Scholar 

Aharonovich D, Sher D. Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals. ISME J. 2016;10:2892–906.

PubMed  PubMed Central  Google Scholar 

Kim W, Levy SB, Foster KR. Rapid radiation in bacteria leads to a division of labour. Nat Commun. 2016;7:10508.

PubMed  PubMed Central  Google Scholar 

Venturelli OS, Carr AV, Fisher G, Hsu RH, Lau R, Bowen BP, et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol Syst Biol. 2018;14:e8157.

PubMed  PubMed Central  Google Scholar 

Little AE, Robinson CJ, Peterson SB, Raffa KF, Handelsman J. Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol. 2008;62:375–401.

PubMed  Google Scholar 

West SA, Diggle SP, Buckling A, Gardner A, Griffin AS. The social lives of microbes. Annu Rev Ecol Evol Syst. 2007;38:53–7.

Google Scholar 

Foster KR, Bell T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr Biol. 2012;22:1845–50.

PubMed  Google Scholar 

Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014;8:894–907.

PubMed  Google Scholar 

Zengler K, Zaramela LS. The social network of microorganisms—how auxotrophies shape complex communities. Nat Rev Microbiol. 2018;16:383–90.

PubMed  PubMed Central  Google Scholar 

Russel J, Røder HL, Madsen JS, Burmølle M, Sørensen SJ. Antagonism correlates with metabolic similarity in diverse bacteria. Proc Natl Acad Sci. 2017;114:10684–8.

PubMed  Google Scholar 

Nielsen AT, Tolker-Nielsen T, Barken KB, Molin S. Role of commensal relationships on the spatial structure of a surface-attached microbial consortium. Environ Microbiol. 2000;2:59–68.

PubMed  Google Scholar 

Hansen SK, Rainey PB, Haagensen JAJ, Molin S. Evolution of species interactions in a biofilm community. Nature. 2007;445:533–6.

PubMed  Google Scholar 

Leinweber A, Fredrik Inglis R, Kümmerli R. Cheating fosters species co-existence in well-mixed bacterial communities. ISME J. 2017;11:1179–88.

PubMed  PubMed Central  Google Scholar 

Fazzino L, Anisman J, Chacón JM, Heineman RH, Harcombe WR. Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community. ISME J. 2020;14:123–34.

PubMed  Google Scholar 

Gao CH, Zhang M, Wu Y, Huang Q, Cai P. Divergent influence to a pathogen invader by resident bacteria with different social interactions. Micro Ecol. 2019;77:76–86.

Google Scholar 

Molina-Santiago C, Udaondo Z, Cordero BF, Ramos JL. Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli. Environ Microbiol Rep. 2017;9:441–8.

PubMed  Google Scholar 

Mallon CA, Le Roux X, van Doorn GS, Dini-Andreote F, Poly F, Salles JF. The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISME J. 2018;12:728–41.

PubMed  PubMed Central  Google Scholar 

Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecol Package. 2007;10:631–7.

Google Scholar 

Wickham H. Ggplot2: elegant graphics for data analysis. New York, USA: Springer Publishing Company; 2009.

Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.

Google Scholar 

Ren D, Madsen JS, de la Cruz-Perera CI, Bergmark L, Sørensen SJ, Burmølle M. High-throughput screening of multispecies biofilm formation and quantitative PCR-based assessment of individual species proportions, useful for exploring interspecific bacterial interactions. Micro Ecol. 2014;68:146–54.

Google Scholar 

Madsen JS, Røder HL, Russel J, Sørensen H, Burmølle M, Sørensen SJ. Coexistence facilitates interspecific biofilm formation in complex microbial communities. Environ Microbiol. 2016;18:2565–74.

PubMed  Google Scholar 

Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010;8:15–25.

PubMed  PubMed Central  Google Scholar 

Szamosvári D, Rütschlin S, Böttcher T. From pirates and killers: does metabolite diversity drive bacterial competition? Org Biomol Chem. 2018;16:2814–9.

PubMed  Google Scholar 

Burmølle M, Ren D, Bjarnsholt T, Sørensen SJ. Interactions in multispecies biofilms: do they actually matter? Trends Microbiol. 2014;22:84–91.

PubMed  Google Scholar 

Hansen LB, Ren D, Burmølle M, Sørensen SJ. Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation. ISME J. 2017;11:300–3.

PubMed  Google Scholar 

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, et al. Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. Nat Microbiol. 2018;3:1274–84.

PubMed  PubMed Central  Google Scholar 

Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, et al. Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun. 2011;2:589.

PubMed  Google Scholar 

Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, et al. Emergent simplicity in microbial community assembly. Science. 2018;361:469–74.

PubMed  PubMed Central  Google Scholar 

Røder HL, Sørensen SJ, Burmølle M. Studying bacterial multispecies biofilms: where to start? Trends Microbiol. 2016;24:503–13.

PubMed  Google Scholar 

Munna MS, Zeba Z, Noor R. Influence of temperature on the growth of Pseudomonas putida. Stamford J Microbiol. 2015;5:9–12.

Google Scholar 

Gonthier A, Guerin-Faublee V, Tilly B, Delignette-Muller ML. Optimal growth temperature of O157 and non-O157 Escherichia coli strains. Lett Appl Microbiol. 2001;33:352–6.

PubMed  Google Scholar 

Van Elsas JD, Semenov AV, Costa R, Trevors JT. Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J. 2011;5:173–83.

PubMed  Google Scholar