Bear A, Rand DG. Intuition, deliberation, and the evolution of cooperation. Proc Natl Acad Sci USA. 2016;113:936–41.
Google Scholar
Athena Aktipis C, Boddy AM, Jansen G, Hibner U, Hochberg ME, Maley CC, et al. Cancer across the tree of life: Cooperation and cheating in multicellularity. Philos Trans R Soc B Biol Sci. 2015;370:20140219.
Google Scholar
D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep. 2018;35:455–88.
Google Scholar
West SA, Diggle SP, Buckling A, Gardner A, Griffin AS. The social lives of microbes. Annu Rev Ecol Evol Syst. 2007;38:53–77.
Google Scholar
Cremer J, Melbinger A, Wienand K, Henriquez T, Jung H, Frey E. Cooperation in microbial populations: theory and experimental model systems. J Mol Biol. 2019;431:4599–644.
Google Scholar
West SA, Cooper GA. Division of labour in microorganisms: an evolutionary perspective. Nat Rev Microbiol. 2016;14:716–23.
Google Scholar
Travisano M, Velicer GJ. Strategies of microbial cheater control. Trends Microbiol. 2004;12:72–8.
Google Scholar
Nadell CD, Drescher K, Foster KR. Spatial structure, cooperation and competition in biofilms. Nat Rev Microbiol. 2016;14:589–600.
Google Scholar
Birch J. Are kin and group selection rivals or friends? Curr Biol. 2019;29:R433–R438.
Google Scholar
Harcombe W. Novel cooperation experimentally evolved between species. Evolution (N. Y). 2010;64:2166–72.
Dobay A, Bagheri HC, Messina A, Kümmerli R, Rankin DJ. Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes. J Evol Biol. 2014;27:1869–77.
Google Scholar
MacLean RC, Gudelj I. Resource competition and social conflict in experimental populations of yeast. Nature. 2006;441:498–501.
Google Scholar
Pande S, Kaftan F, Lang S, Svatoš A, Germerodt S, Kost C. Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments. ISME J. 2016;10:1413–23.
Google Scholar
Kreft J-U. Biofilms promote altruism. Microbiology. 2004;150:2751–60.
Google Scholar
Chuang JS, Rivoire O, Leibler S. Simpson’s paradox in a synthetic microbial system. Science. 2009;323:272–6.
Google Scholar
Hsu RH, Clark RL, Tan JW, Ahn JC, Gupta S, Romero PA, et al. Microbial interaction network inference in microfluidic droplets. Cell Syst. 2019;9:229–42.
Google Scholar
Park J, Kerner A, Burns MA, Lin XN Microdroplet-enabled highly parallel co-cultivation of microbial communities. PLoS One. 2011;6:e17019.
Wilson CE, Lopatkin AJ, Craddock TJA, Driscoll WW, Eldakar OT, Lopez JV, et al. Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria. Sci Rep. 2017;7:1–13.
Hauert C, Doebeli M. Spatial structure often inhibits the evolution of cooperation in the snowdrift game. Nature. 2004;428:643–6.
Google Scholar
Rebolleda-Gómez M, Travisano M The cost of being big: local competition, importance of dispersal, and experimental evolution of reversal to unicellularity. Am Nat. 2018;192:731–44.
Sieuwerts S, Molenaar D, SAFT VanHijum, Beerthuyzen M, MJA Stevens, PWM Janssen, et al. Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol. 2010;76:7775–84.
Google Scholar
Blasche S, Kim Y, Mars R, Kafkia E, Maansson M, Machado D, et al. Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning. bioRxiv 2019;541870.
Gobbetti M, Corsetti A, Rossi J. The sourdough microflora. Interactions of lactic acid bacteria and yeasts: metabolism of amino acids. World J Microbiol Biotechnol. 1994;10:275–9.
Google Scholar
Müller MJI, Neugeboren BI, Nelson DR, Murray AW. Genetic drift opposes mutualism during spatial population expansion. Proc Natl Acad Sci USA. 2014;111:1037–42.
Google Scholar
Inglis RF, Biernaskie JM, Gardner A, Kümmerli R. Presence of a loner strain maintains cooperation and diversity in well-mixed bacterial communities. Proc R Soc B Biol Sci. 2016;283:20152682.
Google Scholar
García J, Traulsen A. Leaving the loners alone: Evolution of cooperation in the presence of antisocial punishment. J Theor Biol. 2012;307:168–73.
Google Scholar
Bachmann H, Fischlechner M, Rabbers I, Barfa N, Branco dos Santos F, Molenaar D, et al. Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci. 2013;110:14302–7.
Google Scholar
Bull JJ, Harcombe WR Population dynamics constrain the cooperative evolution of cross-feeding. PLoS One. 2009;4:e4115.
Smith JM. Group selection and kin selection. Nature. 1964;201:1145–7.
Google Scholar
Otto R, ten Brink B, Veldkamp H, Konings WN. The relation between growth rate and electrochemical proton gradient of Streptococcus cremoris. FEMS Microbiol Lett. 1983;16:69–74.
Google Scholar
Jarvis B, Wilrich C, Wilrich P-T. Reconsideration of the derivation of most probable numbers, their standard deviations, confidence bounds and rarity values. J Appl Microbiol. 2010;109:1660–7.
Google Scholar
Pool WA, Neves AR, Kok J, Santos H, Kuipers OP. Natural sweetening of food products by engineering Lactococcus lactis for glucose production. Metab Eng. 2006;8:456–64.
Google Scholar
Leenhouts KJ, Gietema J, Kok J, Venema G. Chromosomal stabilization of the proteinase genes in Lactococcus lactis. Appl Environ Microbiol. 1991;57:2568–75.
Google Scholar
Bachmann H, Kleerebezem M, Van Hylckama Vlieg JET. High-throughput identification and validation of in situ-expressed genes of Lactococcus lactis. Appl Environ Microbiol. 2008;74:4727–36.
Google Scholar
Nordkvist M, Jensen NBS, Villadsen J. Glucose metabolism in Lactococcus lactis MG1363 under different aeration conditions: Requirement of acetate to sustain growth under microaerobic conditions. Appl Environ Microbiol. 2003;69:3462–8.
Google Scholar
Price CE, Branco Dos Santos F, Hesseling A, Uusitalo JJ, Bachmann H, Benavente V, et al. Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evol Biol. 2019;19:1–15.
Google Scholar
Wilson DS. A theory of group selection. Proc Natl Acad Sci USA. 1975;72:143–6.
Google Scholar
Rumbaugh KP, Sauer K Biofilm dispersion. Nat Rev Microbiol. 2020;18:571–86.
Morris JJ. Black queen evolution: the role of leakiness in structuring microbial communities. Trends Genet. 2015;31:475–82.
Google Scholar
Bachmann H, Molenaar D, Kleerebezem M, van Hylckama Vlieg JET. High local substrate availability stabilizes a cooperative trait. ISME J. 2011;5:929–32.
Google Scholar
Gore J, Youk H, van Oudenaarden A. Snowdrift game dynamics and facultative cheating in yeast. Nature. 2009;459:253–6.
Google Scholar
Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science (80-). 2001;292:504–7.
Google Scholar
Marchal M, Goldschmidt F, Derksen-Müller SN, Panke S, Ackermann M, Johnson DR A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evol Biol. 2017;17:1–14.
Preussger D, Giri S, Muhsal LK, Oña L, Kost C Reciprocal fitness feedbacks promote the evolution of mutualistic cooperation. Curr Biol. 2020;30:3580–90.
Harcombe WR, Chacon J, Adamowicz E, Chubiz L, Marx C Evolution of bidirectional costly mutualism from byproduct consumption. PNAS 2018;115.
Pacheco AR, Moel M, Segrè D Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun 2019;10:1–12.
Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, et al. Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow. Cell Syst. 2017;5:345–57.
Google Scholar
Pillai P, Gouhier TC, Vollmer SV. The cryptic role of biodiversity in the emergence of host-microbial mutualisms. Ecol Lett. 2014;17:1437–46.
Google Scholar
van Tatenhove-Pel RJ, Rijavec T, Lapanje A, van Swam I, Zwering E, Hernandez-Valdes JA, et al. Microbial competition reduces metabolic interaction distances to the low µm-range. ISME J. 2021;15:688–701.
Co AD, van Vliet S, Kiviet DJ, Schlegel S, Ackermann M. Short-range interactions govern the dynamics and functions of microbial communities. Nat Ecol Evol. 2020;4:366–75.
Google Scholar
Saleski TE, Kerner AR, Chung MT, Jackman CM, Khasbaatar A, Kurabayashi K, et al. Synthrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metab Eng. 2019;54:232–43.
Google Scholar
Sung YJ, Young JHK, Choi H Il, Kwak HS, Sim SJ Magnetophoretic sorting of microdroplets with different microalgal cell densities for rapid isolation of fast growing strains. Sci Rep. 2017;7:1–11.
Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, et al. Cultivating the uncultured. Proc Natl Acad Sci USA. 2002;99:15681–6.
Google Scholar
Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, et al. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci USA. 2019;116:12804–9.
Google Scholar
Riehl C, Frederickson ME Cheating and punishment in cooperative animal societies. Philos Trans R Soc B Biol Sci. 2016;371:20150090.
Nepi M, Grasso DA, Mancuso S. Nectar in plant–insect mutualistic relationships: From food reward to partner manipulation. Front Plant Sci. 2018;9:1–14.
Google Scholar
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