Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).
Article CAS PubMed Google Scholar
Mueller, U. G. & Sachs, J. L. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 23, 606–617 (2015).
Article CAS PubMed Google Scholar
Schloss, P. et al. Status of the archaeal and bacterial census: an update. mBio 7, e00201–e00216 (2016).
Article CAS PubMed PubMed Central Google Scholar
Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009).
Article CAS PubMed Google Scholar
Oña, L. et al. Obligate cross-feeding expands the metabolic niche of bacteria. Nat. Ecol. Evol. 5, 1224–1232 (2020).
Riley, M. A. in Prokaryotic Antimicrobial Peptides: from Genes to Applications (eds Drider, D. & Rebuffat, S.) 13–26 (Springer, 2011).
Coulthurst, S. The Type VI secretion system: a versatile bacterial weapon. Microbiology 165, 503–515 (2019).
Article CAS PubMed Google Scholar
West, S. A., Griffin, A. S., Gardner, A. & Diggle, S. P. Social evolution theory for microorganisms. Nat. Rev. Microbiol. 4, 597–607 (2006).
Article CAS PubMed Google Scholar
Rosenzweig, R. F., Sharp, R. R., Treves, D. S. & Adams, J. Microbial evolution in a simple unstructured environment - genetic differentiation in Escherichia coli. Genetics 137, 903–917 (1994).
Article CAS PubMed PubMed Central Google Scholar
Pauli, B., Ajmera, S. & Kost, C. Determinants of synergistic cell-cell interactions in bacteria. Biol. Chem. 404, 521–534 (2023).
Article CAS PubMed Google Scholar
Giovannoni, S. J. Vitamins in the sea. Proc. Natl Acad. Sci. USA 109, 13888–13889 (2012).
Article CAS PubMed PubMed Central Google Scholar
D’Souza, G. et al. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat. Prod. Rep. 35, 455–488 (2018).
Enke, T. N. et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr. Biol. 29, 1528–1535 (2019).
Article CAS PubMed Google Scholar
Kim, S. et al. Heme auxotrophy in abundant aquatic microbial lineages. Proc. Natl Acad. Sci. USA 118, e2102750118 (2021).
Article CAS PubMed PubMed Central Google Scholar
Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25 (2010).
Article CAS PubMed PubMed Central Google Scholar
Foster, K. R. & Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845–1850 (2012).
Article CAS PubMed Google Scholar
Palmer, J. D. & Foster, K. R. Bacterial species rarely work together. Science 376, 581–582 (2022).
Article CAS PubMed Google Scholar
Ortiz, A., Vega, N. M., Ratzke, C. & Gore, J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. ISME J. 15, 2131–2145 (2021).
Article CAS PubMed PubMed Central Google Scholar
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Article PubMed PubMed Central Google Scholar
Ghoul, M. & Mitri, S. The ecology and evolution of microbial competition. Trends Microbiol. 24, 833–845 (2016).
Article CAS PubMed Google Scholar
Mee, M. T., Collins, J. J., Church, G. M. & Wang, H. H. Syntrophic exchange in synthetic microbial communities. Proc. Natl Acad. Sci. USA 111, E2149–E2156 (2014).
Article CAS PubMed PubMed Central Google Scholar
D’Souza, G. et al. Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria. Evolution 68, 2559–2570 (2014).
Embree, M., Liu, J. K., Al-Bassam, M. M. & Zengler, K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc. Natl Acad. Sci. USA 112, 15450–15455 (2015).
Article CAS PubMed PubMed Central Google Scholar
Yu, J. S. L. et al. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance. Nat. Microbiol. 7, 542–555 (2022).
Article CAS PubMed PubMed Central Google Scholar
Hessler, T. et al. Vitamin interdependencies predicted by metagenomics-informed network analyses validated in microbial community microcosms. Nat. Commun. 14, 4768 (2023).
Article CAS PubMed PubMed Central Google Scholar
Lochhead, A. G. & Burton, M. O. Qualitative studies of soil microorganisms .14. Specific vitamin requirements of the predominant bacterial flora. Can. J. Microbiol. 3, 35–42 (1957).
Article CAS PubMed Google Scholar
Zatsarinnaya, E. A., Kalchugina, V. D. & Kolupaeva, N. V. Occurrence of auxotrophic variants among bacteria of Enterobacteriaceae family isolated from water objects of the north-west of the Murmansk region. IOP Conf. Ser. Earth Environ. Sci. 263, 012036 (2019).
Ryback, B., Bortfeld-Miller, M. & Vorholt, J. A. Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria. ISME J. 16, 2712–2724 (2022).
Article CAS PubMed PubMed Central Google Scholar
Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).
Article PubMed PubMed Central Google Scholar
Figueroa-Gonzalez, P. A. et al. Saccharibacteria as organic carbon sinks in hydrocarbon-fueled communities. Front. Microbiol. 11, 587782 (2020).
Article PubMed PubMed Central Google Scholar
Hubalek, V. et al. Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic conditions. mSystems 2, e00038-17 (2017).
Article PubMed PubMed Central Google Scholar
Rodríguez-Gijón, A. et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy. Front. Microbiol. 12, 761869 (2022).
Article PubMed PubMed Central Google Scholar
Moura, A., Savageau, M. A. & Alves, R. Relative amino acid composition signatures of organisms and environments. PLoS ONE 8, e77319 (2013).
Article CAS PubMed PubMed Central Google Scholar
Nagata, T. in Microbial Ecology of the Oceans 2nd edn (ed. Kirchman D. L.) 207–241 (Wiley, 2008).
Canon, F. et al. Understanding the mechanisms of positive microbial interactions that benefit lactic acid bacteria co-cultures. Front. Microbiol. 11, 2088 (2020).
Article PubMed PubMed Central Google Scholar
Blasche, S. et al. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nat. Microbiol. 6, 196–208 (2021).
Article CAS PubMed PubMed Central Google Scholar
Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).
Article CAS PubMed PubMed Central Google Scholar
Durham, B. P. et al. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environ. Microbiol. 19, 3500–3513 (2017).
Article CAS PubMed Google Scholar
Piccardi, P., Vessman, B. & Mitri, S. Toxicity drives facilitation between 4 bacterial species. Proc. Natl Acad. Sci. USA 116, 15979 (2019).
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