1932

Abstract

For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-micro-032521-041956
2023-09-15
2024-06-17
Loading full text...

Full text loading...

/deliver/fulltext/micro/77/1/annurev-micro-032521-041956.html?itemId=/content/journals/10.1146/annurev-micro-032521-041956&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Adesulu A, Awojobi KO. 2014. Enhancing sustainable development through indigenous fermented food products in Nigeria. Afr. J. Microbiol. Res. 8:1338–43
    [Google Scholar]
  2. 2.
    Arora K, Ameur H, Polo A, Di Cagno R, Rizzello CG, Gobbetti M. 2021. Thirty years of knowledge on sourdough fermentation: a systematic review. Trends Food Sci. Technol. 108:71–83
    [Google Scholar]
  3. 3.
    Bachmann H, Molenaar D, Branco Dos Santos F, Teusink B 2017. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol. Rev. 41:Suppl. 1S201–19
    [Google Scholar]
  4. 4.
    Bachmann H, Starrenburg MJC, Molenaar D, Kleerebezem M, van Hylckama Vlieg JET. 2012. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res. 22:1115–24
    [Google Scholar]
  5. 5.
    Beresford T, Williams A 2004. The microbiology of cheese ripening. Cheese: Chemistry, Physics and Microbiology, Vol. 1 General Aspects PF Fox, PLH McSweeney, TM Cogan, TP Guinee 287–317. London: Academic
    [Google Scholar]
  6. 6.
    Bertuzzi AS, Walsh AM, Sheehan JJ, Cotter PD, Crispie F et al. 2018. Omics-based insights into flavor development and microbial succession within surface-ripened cheese. mSystems 3:1e00211–17
    [Google Scholar]
  7. 7.
    Biango-Daniels MN, Wolfe BE. 2021. American artisan cheese quality and spoilage: a survey of cheesemakers’ concerns and needs. J. Dairy Sci. 104:56283–94
    [Google Scholar]
  8. 8.
    Blasche S, Kim Y, Mars RAT, Machado D, Maansson M et al. 2021. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nat. Microbiol. 6:196–208
    [Google Scholar]
  9. 9.
    Bodinaku I, Shaffer J, Connors AB, Steenwyk JL, Biango-Daniels MN et al. 2019. Rapid phenotypic and metabolomic domestication of wild penicillium molds on cheese. mBio 10:5e02445–19
    [Google Scholar]
  10. 10.
    Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K et al. 2015. Microbial biogeography of the transnational fermented milk matsoni. Food Microbiol. 50:12–19
    [Google Scholar]
  11. 11.
    Bokulich NA, Bergsveinson J, Ziola B, Mills DA. 2015. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. eLife 4:e04634
    [Google Scholar]
  12. 12.
    Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA. 2016. A new perspective on microbial landscapes within food production. Curr. Opin. Biotechnol. 37:182–89
    [Google Scholar]
  13. 13.
    Bokulich NA, Mills DA. 2012. Next-generation approaches to the microbial ecology of food fermentations. BMB Rep. 45:7377–89
    [Google Scholar]
  14. 14.
    Bokulich NA, Mills DA. 2013. Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl. Environ. Microbiol. 79:175214–23
    [Google Scholar]
  15. 15.
    Bokulich NA, Ohta M, Lee M, Mills DA. 2014. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Appl. Environ. Microbiol. 80:175522–29
    [Google Scholar]
  16. 16.
    Bokulich NA, Thorngate JH, Richardson PM, Mills DA. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. PNAS 111:1E139–48
    [Google Scholar]
  17. 17.
    Castledine M, Padfield D, Buckling A. 2020. Experimental (co)evolution in a multi-species microbial community results in local maladaptation. Ecol. Lett. 23:111673–81
    [Google Scholar]
  18. 18.
    Chang C-Y, Vila JCC, Bender M, Li R, Mankowski MC et al. 2021. Engineering complex communities by directed evolution. Nat. Ecol. Evol. 5:71011–23
    [Google Scholar]
  19. 19.
    Chang H-W, Kim K-H, Nam Y-D, Roh SW, Kim M-S et al. 2008. Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 126:1–2159–66
    [Google Scholar]
  20. 20.
    Clark CJ, Poulsen JR, Levey DJ, Osenberg CW. 2007. Are plant populations seed limited? A critique and meta-analysis of seed addition experiments. Am. Nat. 170:1128–42
    [Google Scholar]
  21. 21.
    Cosetta CM, Kfoury N, Robbat A, Wolfe BE. 2020. Fungal volatiles mediate cheese rind microbiome assembly. Environ. Microbiol. 22:114745–60
    [Google Scholar]
  22. 22.
    Cosetta CM, Wolfe BE. 2019. Causes and consequences of biotic interactions within microbiomes. Curr. Opin. Microbiol. 50:35–41
    [Google Scholar]
  23. 23.
    D'Amico DJ, Donnelly CW. 2017. Growth and survival of microbial pathogens in cheese. Cheese PLH McSweeney, PF Fox, PD Cotter, DW Everett 573–94. London: Academic
    [Google Scholar]
  24. 24.
    De Vuyst L, Leroy F. 2007. Bacteriocins from lactic acid bacteria: production, purification, and food applications. J. Mol. Microbiol. Biotechnol. 13:4194–99
    [Google Scholar]
  25. 25.
    De Vuyst L, Van Kerrebroeck S, Harth H, Huys G, Daniel H-M, Weckx S. 2014. Microbial ecology of sourdough fermentations: diverse or uniform?. Food Microbiol. 37:11–29
    [Google Scholar]
  26. 26.
    De Vuyst L, Vrancken G, Ravyts F, Rimaux T, Weckx S. 2009. Biodiversity, ecological determinants, and metabolic exploitation of sourdough microbiota. Food Microbiol. 26:7666–75
    [Google Scholar]
  27. 27.
    Di Cagno R, Coda R, De Angelis M, Gobbetti M. 2013. Exploitation of vegetables and fruits through lactic acid fermentation. Food Microbiol. 33:11–10
    [Google Scholar]
  28. 28.
    Dobson A, O'Sullivan O, Cotter PD, Ross P, Hill C 2011. High-throughput sequence-based analysis of the bacterial composition of kefir and an associated kefir grain. FEMS Microbiol. Lett. 320:156–62
    [Google Scholar]
  29. 29.
    Dunn RR, Wilson J, Nichols LM, Gavin MC. 2021. Toward a global ecology of fermented foods. Curr. Anthropol. 62:S24S220–32
    [Google Scholar]
  30. 30.
    Einson JE, Rani A, You X, Rodriguez AA, Randell CL et al. 2018. A vegetable fermentation facility hosts distinct microbiomes reflecting the production environment. Appl. Environ. Microbiol. 84:22e01680–18
    [Google Scholar]
  31. 31.
    Ercolini D, Pontonio E, De Filippis F, Minervini F, La Storia A et al. 2013. Microbial ecology dynamics during rye and wheat sourdough preparation. Appl. Environ. Microbiol. 79:247827–36
    [Google Scholar]
  32. 32.
    Falardeau J, Keeney K, Trmčić A, Kitts D, Wang S. 2019. Farm-to-fork profiling of bacterial communities associated with an artisan cheese production facility. Food Microbiol. 83:48–58
    [Google Scholar]
  33. 33.
    Gallone B, Steensels J, Prahl T, Soriaga L, Saels V et al. 2016. Domestication and divergence of Saccharomyces cerevisiae beer yeasts. Cell 166:61397–410.e16
    [Google Scholar]
  34. 34.
    Gänzle M. 2022. The periodic table of fermented foods: limitations and opportunities. Appl. Microbiol. Biotechnol. 106:82815–26
    [Google Scholar]
  35. 35.
    Gänzle M, Ripari V. 2016. Composition and function of sourdough microbiota: from ecological theory to bread quality. Int. J. Food Microbiol. 239:19–25
    [Google Scholar]
  36. 36.
    Gänzle MG, Loponen J, Gobbetti M. 2008. Proteolysis in sourdough fermentations: mechanisms and potential for improved bread quality. Trends Food Sci. Technol. 19:10513–21
    [Google Scholar]
  37. 37.
    Gayevskiy V, Goddard MR. 2012. Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. ISME J. 6:71281–90
    [Google Scholar]
  38. 38.
    Gibbons JG, Rinker DC. 2015. The genomics of microbial domestication in the fermented food environment. Curr. Opin. Genet. Dev. 35:1–8
    [Google Scholar]
  39. 39.
    Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL et al. 2012. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr. Biol. 22:151403–9
    [Google Scholar]
  40. 40.
    Harrison K, Curtin C. 2021. Microbial composition of SCOBY starter cultures used by commercial kombucha brewers in North America. Microorganisms 9:51060
    [Google Scholar]
  41. 41.
    Hittinger CT, Steele JL, Ryder DS. 2018. Diverse yeasts for diverse fermented beverages and foods. Curr. Opin. Biotechnol. 49:199–206
    [Google Scholar]
  42. 42.
    Hutkins RW. 2008. Microbiology and Technology of Fermented Foods New York: John Wiley
    [Google Scholar]
  43. 43.
    Hutkins RW. 2013. Microbiology and Technology of Fermented Foods New York: John Wiley. , 2nd ed..
    [Google Scholar]
  44. 44.
    Irlinger F, Layec S, Hélinck S, Dugat-Bony E. 2015. Cheese rind microbial communities: diversity, composition and origin. FEMS Microbiol. Lett. 362:21–11
    [Google Scholar]
  45. 45.
    Irlinger F, Mounier J. 2009. Microbial interactions in cheese: implications for cheese quality and safety. Curr. Opin. Biotechnol. 20:2142–48
    [Google Scholar]
  46. 46.
    Jung JY, Lee SH, Jeon CO. 2014. Kimchi microflora: history, current status, and perspectives for industrial kimchi production. Appl. Microbiol. Biotechnol. 98:62385–93
    [Google Scholar]
  47. 47.
    Kable ME, Srisengfa Y, Laird M, Zaragoza J, McLeod J et al. 2016. The core and seasonal microbiota of raw bovine milk in tanker trucks and the impact of transfer to a milk processing facility. mBio 7:4e00836–16
    [Google Scholar]
  48. 48.
    Kamelamela N, Zalesne M, Morimoto J, Robbat A, Wolfe BE. 2018. Indigo- and indirubin-producing strains of Proteus and Psychrobacter are associated with purple rind defect in a surface-ripened cheese. Food Microbiol. 76:543–52
    [Google Scholar]
  49. 49.
    Kamimura BA, Cabral L, Noronha MF, Baptista RC, Nascimento HM, Sant'Ana AS 2020. Amplicon sequencing reveals the bacterial diversity in milk, dairy premises and Serra da Canastra artisanal cheeses produced by three different farms. Food Microbiol. 89:103453
    [Google Scholar]
  50. 50.
    Kang SE, Kim MJ, Kim TW. 2019. Diversity and role of yeast on kimchi fermentation. J. Korean Soc. Food Cult. 34:2201–7
    [Google Scholar]
  51. 51.
    Kastman EK, Kamelamela N, Norville JW, Cosetta CM, Dutton RJ, Wolfe BE. 2016. Biotic interactions shape the ecological distributions of Staphylococcus species. mBio 7:5e01157–16. Erratum 2017. mBio 8:2e00329–17
    [Google Scholar]
  52. 52.
    Kembel SW, Jones E, Kline J, Northcutt D, Stenson J et al. 2012. Architectural design influences the diversity and structure of the built environment microbiome. ISME J. 6:81469–79
    [Google Scholar]
  53. 53.
    Klaenhammer TR. 1988. Bacteriocins of lactic acid bacteria. Biochimie 70:3337–49
    [Google Scholar]
  54. 54.
    Landis EA, Fogarty E, Edwards JC, Popa O, Eren AM, Wolfe BE. 2022. Microbial diversity and interaction specificity in kombucha tea fermentations. mSystems 7:3e0015722
    [Google Scholar]
  55. 55.
    Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N et al. 2021. The diversity and function of sourdough starter microbiomes. eLife 10:e61644
    [Google Scholar]
  56. 56.
    Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB et al. 2012. Species interactions alter evolutionary responses to a novel environment. PLOS Biol. 10:5e1001330
    [Google Scholar]
  57. 57.
    Lee SH, Whon TW, Roh SW, Jeon CO. 2020. Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches. Appl. Microbiol. Biotechnol. 104:187731–44
    [Google Scholar]
  58. 58.
    Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ et al. 2020. Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants. mSystems 5:6e00522–20
    [Google Scholar]
  59. 59.
    Leite AMO, Miguel MAL, Peixoto RS, Rosado AS, Silva JT, Paschoalin VMF. 2013. Microbiological, technological and therapeutic properties of kefir: a natural probiotic beverage. Braz. J. Microbiol. 44:2341–49
    [Google Scholar]
  60. 60.
    Macori G, Cotter PD. 2018. Novel insights into the microbiology of fermented dairy foods. Curr. Opin. Biotechnol. 49:172–78
    [Google Scholar]
  61. 61.
    Marcellino N, Benson DR. 2013. The good, the bad, and the ugly: tales of mold-ripened cheese. Microbiol. Spectr. 1:1) https://doi.org/10.1128/microbiolspec.CM-0005-12
    [Google Scholar]
  62. 62.
    Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD et al. 2017. Health benefits of fermented foods: microbiota and beyond. Curr. Opin. Biotechnol. 44:94–102
    [Google Scholar]
  63. 63.
    Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD et al. 2021. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat. Rev. Gastroenterol. Hepatol. 18:3196–208
    [Google Scholar]
  64. 64.
    Marsh AJ, Hill C, Ross RP, Cotter PD. 2014. Fermented beverages with health-promoting potential: past and future perspectives. Trends Food Sci. Technol. 38:2113–24
    [Google Scholar]
  65. 65.
    McGovern P, Jalabadze M, Batiuk S, Callahan MP, Smith KE et al. 2017. Early Neolithic wine of Georgia in the South Caucasus. PNAS 114:48E10309–18
    [Google Scholar]
  66. 66.
    Miller ER, Kearns PJ, Niccum BA, O'Mara Schwartz J, Ornstein A, Wolfe BE 2019. Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere. Appl. Environ. Microbiol. 85:13e00269–19
    [Google Scholar]
  67. 67.
    Miller ER, O'Mara Schwartz J, Cox G, Wolfe BE 2020. A gnotobiotic system for studying microbiome assembly in the phyllosphere and in vegetable fermentation. J. Vis. Exp. 160:e61149
    [Google Scholar]
  68. 68.
    Monnet C, Landaud S, Bonnarme P, Swennen D. 2015. Growth and adaptation of microorganisms on the cheese surface. FEMS Microbiol. Lett. 362:11–9
    [Google Scholar]
  69. 69.
    Morrison-Whittle P, Goddard MR. 2018. From vineyard to winery: a source map of microbial diversity driving wine fermentation. Environ. Microbiol. 20:175–84
    [Google Scholar]
  70. 70.
    Mounier J, Goerges S, Gelsomino R, Vancanneyt M, Vandemeulebroecke K et al. 2006. Sources of the adventitious microflora of a smear-ripened cheese. J. Appl. Microbiol. 101:3668–81
    [Google Scholar]
  71. 71.
    Mounier J, Monnet C, Vallaeys T, Arditi R, Sarthou A-S et al. 2008. Microbial interactions within a cheese microbial community. Appl. Environ. Microbiol. 74:1172–81
    [Google Scholar]
  72. 72.
    Nascimento MS, Pena PO, Brum DM, Imazaki FT, Tucci MLS, Efraim P. 2013. Behavior of Salmonella during fermentation, drying and storage of cocoa beans. Int. J. Food Microbiol. 167:3363–68
    [Google Scholar]
  73. 73.
    Nemergut DR, Schmidt SK, Fukami T, O'Neill SP, Bilinski TM et al. 2013. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77:3342–56
    [Google Scholar]
  74. 74.
    Niccum BA, Kastman EK, Kfoury N, Robbat A Jr., Wolfe BE. 2020. Strain-level diversity impacts cheese rind microbiome assembly and function. mSystems 5:3e00149–20
    [Google Scholar]
  75. 75.
    Obafemi YD, Oranusi SU, Ajanaku KO, Akinduti PA, Leech J, Cotter PD. 2022. African fermented foods: overview, emerging benefits, and novel approaches to microbiome profiling. npj Sci. Food 6:115
    [Google Scholar]
  76. 76.
    Parente E, Cogan TM. 2004. Starter cultures: general aspects. Cheese Chem. Phys. Microbiol. 1:123–48
    [Google Scholar]
  77. 77.
    Pažin V, Jankuloski D, Kozačinski L, Dobranić V, Njari B et al. 2018. Tracing of Listeria monocytogenes contamination routes in fermented sausage production chain by pulsed-field gel electrophoresis typing. Foods 7:12198
    [Google Scholar]
  78. 78.
    Peñas E, Martinez-Villaluenga C, Frias J. 2017. Sauerkraut: production, composition, and health benefits. Fermented Foods in Health and Disease Prevention J Frias, C Martinez-Villaluenga, E Peñas 557–76. Boston: Academic
    [Google Scholar]
  79. 79.
    Pierce EC, Dutton RJ. 2022. Putting microbial interactions back into community contexts. Curr. Opin. Microbiol. 65:56–63
    [Google Scholar]
  80. 80.
    Pierce EC, Morin M, Little JC, Liu RB, Tannous J et al. 2021. Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. Nat. Microbiol. 6:187–102
    [Google Scholar]
  81. 81.
    Primack RB, Miao SL. 1992. Dispersal can limit local plant distribution. Conserv. Biol. 6:4513–19
    [Google Scholar]
  82. 82.
    Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD 2011. Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese. Int. J. Food Microbiol. 150:2–381–94
    [Google Scholar]
  83. 83.
    Raynaud T, Blouin M, Devers-Lamrani M, Garmyn D, Spor A. 2022. The central role of the interspecific interactions in the evolution of microbial communities. Preprint, bioRxiv. https://www.biorxiv.org/content/10.1101/2022.01.17.476584v1
  84. 84.
    Reese AT, Madden AA, Joossens M, Lacaze G, Dunn RR. 2020. Influences of ingredients and bakers on the bacteria and fungi in sourdough starters and bread. mSphere 5:1e00950–19
    [Google Scholar]
  85. 85.
    Rezac S, Kok CR, Heermann M, Hutkins R. 2018. Fermented foods as a dietary source of live organisms. Front. Microbiol. 9:1785
    [Google Scholar]
  86. 86.
    Rizo J, Guillén D, Farrés A, Díaz-Ruiz G, Sánchez S et al. 2020. Omics in traditional vegetable fermented foods and beverages. Crit. Rev. Food Sci. Nutr. 60:5791–809
    [Google Scholar]
  87. 87.
    Rizzello CG, Cavoski I, Turk J, Ercolini D, Nionelli L et al. 2015. Organic cultivation of Triticum turgidum subsp. durum is reflected in the flour-sourdough fermentation-bread axis. Appl. Environ. Microbiol. 81:93192–204
    [Google Scholar]
  88. 88.
    Rogalski E, Ehrmann MA, Vogel RF. 2021. Intraspecies diversity and genome-phenotype-associations in Fructilactobacillus sanfranciscensis. Microbiol. Res. 243:126625
    [Google Scholar]
  89. 89.
    Romulo A, Surya R. 2021. Tempe: A traditional fermented food of Indonesia and its health benefits. Int. J. Gastronomy Food Sci. 26:100413
    [Google Scholar]
  90. 90.
    Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M et al. 2020. Domestication of the emblematic white cheese-making fungus Penicillium camemberti and its diversification into two varieties. Curr. Biol. 30:224441–53.e4
    [Google Scholar]
  91. 91.
    Rosa DD, Dias MMS, Grześkowiak ŁM, Reis SA, Conceição LL, Peluzio MCG. 2017. Milk kefir: nutritional, microbiological and health benefits. Nutr. Res. Rev. 30:182–96
    [Google Scholar]
  92. 92.
    Ross RP, Morgan S, Hill C. 2002. Preservation and fermentation: past, present and future. Int. J. Food Microbiol. 79:1–23–16
    [Google Scholar]
  93. 93.
    Roy B, Kala CP, Farooquee NA, Majila BS. 2004. Indigenous fermented food and beverages: a potential for economic development of the high altitude societies in Uttaranchal. J. Hum. Ecol. 15:145–49
    [Google Scholar]
  94. 94.
    Saak CC, Pierce EC, Dinh CB, Portik D, Hall R et al. 2023. Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities. Food Microbiol. 8:1e00701–22
    [Google Scholar]
  95. 95.
    Satora P, Skotniczny M, Strnad S, Ženišová K. 2020. Yeast microbiota during sauerkraut fermentation and its characteristics. Int. J. Mol. Sci. 21:249699
    [Google Scholar]
  96. 96.
    Scherlach K, Graupner K, Hertweck C. 2013. Molecular bacteria-fungi interactions: effects on environment, food, and medicine. Annu. Rev. Microbiol. 67:375–97
    [Google Scholar]
  97. 97.
    Sieuwerts S, de Bok FAM, Hugenholtz J, van Hylckama Vlieg JET. 2008. Unraveling microbial interactions in food fermentations: from classical to genomics approaches. Appl. Environ. Microbiol. 74:164997–5007
    [Google Scholar]
  98. 98.
    Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HTK et al. 2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ. Microbiol. 12:3758–73
    [Google Scholar]
  99. 99.
    Sloan WT, Nnaji CF, Lunn M, Curtis TP, Colloms SD et al. 2021. Drift dynamics in microbial communities and the effective community size. Environ. Microbiol. 23:52473–83
    [Google Scholar]
  100. 100.
    Soininen J, McDonald R, Hillebrand H. 2007. The distance decay of similarity in ecological communities. Ecography 30:13–12
    [Google Scholar]
  101. 101.
    Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW et al. 2013. Quantifying community assembly processes and identifying features that impose them. ISME J. 7:112069–79
    [Google Scholar]
  102. 102.
    Steinkraus K 1995. Handbook of Indigenous Fermented Foods. New York: Marcel Dekker. , 2nd ed..
    [Google Scholar]
  103. 103.
    Sun L, D'Amico DJ. 2021. Composition, succession, and source tracking of microbial communities throughout the traditional production of a farmstead cheese. mSystems 6:5e0083021
    [Google Scholar]
  104. 104.
    Sundarraman D, Hay EA, Martins DM, Shields DS, Pettinari NL, Parthasarathy R. 2020. Higher-order interactions dampen pairwise competition in the zebrafish gut microbiome. mBio 11:5e01667–20
    [Google Scholar]
  105. 105.
    Tamang JP 2010. Diversity of fermented foods. Fermented Foods and Beverages of the World JP Tamang, K Kailasapathy, chap. 2 Boca Raton, FL: CRC
    [Google Scholar]
  106. 106.
    Tamang JP, Cotter PD, Endo A, Han NS, Kort R et al. 2020. Fermented foods in a global age: East meets West. Compr. Rev. Food Sci. Food Saf. 19:1184–217
    [Google Scholar]
  107. 107.
    Tamang JP, Watanabe K, Holzapfel WH. 2016. Review: diversity of microorganisms in global fermented foods and beverages. Front. Microbiol. 7:377
    [Google Scholar]
  108. 108.
    Tofalo R, Fusco V, Böhnlein C, Kabisch J, Logrieco AF et al. 2020. The life and times of yeasts in traditional food fermentations. Crit. Rev. Food Sci. Nutr. 60:183103–32
    [Google Scholar]
  109. 109.
    van Hijum SAFT, Vaughan EE, Vogel RF. 2013. Application of state-of-art sequencing technologies to indigenous food fermentations. Curr. Opin. Biotechnol. 24:2178–86
    [Google Scholar]
  110. 110.
    Vellend M. 2010. Conceptual synthesis in community ecology. Q. Rev. Biol. 85:2183–206
    [Google Scholar]
  111. 111.
    Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD et al. 2021. Gut-microbiota-targeted diets modulate human immune status. Cell 184:164137–53.e14
    [Google Scholar]
  112. 112.
    Winters M, Panayotides D, Bayrak M, Rémont G, Viejo CG et al. 2019. Defined co-cultures of yeast and bacteria modify the aroma, crumb and sensory properties of bread. J. Appl. Microbiol. 127:3778–93
    [Google Scholar]
  113. 113.
    Wolfe BE, Button JE, Santarelli M, Dutton RJ. 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158:2422–33
    [Google Scholar]
  114. 114.
    Wolfe BE, Dutton RJ. 2015. Fermented foods as experimentally tractable microbial ecosystems. Cell 161:149–55
    [Google Scholar]
  115. 115.
    Xue Z, Brooks JT, Quart Z, Stevens ET, Kable ME et al. 2021. Microbiota assessments for the identification and confirmation of slit defect-causing bacteria in milk and cheddar cheese. mSystems 6:1e01114–20
    [Google Scholar]
  116. 116.
    Yeluri Jonnala BR, McSweeney PLH, Sheehan JJ, Cotter PD 2018. Sequencing of the cheese microbiome and its relevance to industry. Front. Microbiol. 9:1020
    [Google Scholar]
  117. 117.
    Yu AO, Leveau JHJ, Marco ML. 2020. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. Environ. Microbiol. Rep. 12:116–29
    [Google Scholar]
  118. 118.
    Zabat MA, Sano WH, Wurster JI, Cabral DJ, Belenky P. 2018. Microbial community analysis of sauerkraut fermentation reveals a stable and rapidly established community. Foods 7:577
    [Google Scholar]
  119. 119.
    Zhang Y, Kastman EK, Guasto JS, Wolfe BE. 2018. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat. Commun. 9:1336
    [Google Scholar]
/content/journals/10.1146/annurev-micro-032521-041956
Loading
/content/journals/10.1146/annurev-micro-032521-041956
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error