Microbial interactions and ecology in fermented food ecosystems

Boethius, A. Something rotten in Scandinavia: the world’s earliest evidence of fermentation. J. Archaeol. Sci. 66, 169–180 (2016).

Article  Google Scholar 

McGovern, P. E. et al. Fermented beverages of pre- and proto-historic China. Proc. Natl Acad. Sci. USA 101, 17593–17598 (2004).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miller, E. R. et al. Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere. Appl. Environ. Microbiol. 85, e00269–19 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma, Y. et al. Microbiota dynamics and volatile metabolite generation during sausage fermentation. Food Chem. 423, 136297 (2023).

Article  CAS  PubMed  Google Scholar 

Porter, J. R. Louis Pasteur. achievements and disappointments. Bacteriol. Rev. 25, 389–403 (1961).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marco, M. L. et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat. Rev. Gastroenterol. Hepatol. 18, 196–208 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Steinkraus, K. H. in Handbook of Food and Beverage Fermentation Technology (eds Hui, Y. H. et al.) 1–8 (Marcel Dekker, 2004).

Beresford, T. P., Fitzsimons, N. A., Brennan, N. L. & Cogan, T. M. Recent advances in cheese microbiology. Int. Dairy J. 11, 259–274 (2001).

Article  CAS  Google Scholar 

Venturini Copetti, M. Yeasts and molds in fermented food production: an ancient bioprocess. Curr. Opin. Food Sci. 25, 57–61 (2019).

Article  Google Scholar 

Benítez-Cabello, A., Delgado, A. M. & Quintas, C. Main challenges expected from the impact of climate change on microbial biodiversity of table olives: current status and trends. Foods 12, 3712 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Choudoir, M. J., Barberán, A., Menninger, H. L., Dunn, R. R. & Fierer, N. Variation in range size and dispersal capabilities of microbial taxa. Ecology 99, 322–334 (2018).

Article  PubMed  Google Scholar 

Gomes, S. I. F. et al. Microbiota in dung and milk differ between organic and conventional dairy farms. Front. Microbiol. 11, 1746 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Streule, S., Freimüller Leischtfeld, S., Galler, M. & Miescher Schwenninger, S. Monitoring of cocoa post-harvest process practices on a small-farm level at five locations in Ecuador. Heliyon 8, e09628 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Reese, A. T., Madden, A. A., Joossens, M., Lacaze, G. & Dunn, R. R. Influences of ingredients and bakers on the bacteria and fungi in sourdough starters and bread. mSphere 5, e00950–19 (2020). Analysis of potential sources of microorganisms and their influence on composition and function of sourdough communities.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Einson, J. E. et al. A vegetable fermentation facility hosts distinct microbiomes reflecting the production environment. Appl. Environ. Microbiol. 84, e01680–18 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Bokulich, N. A., Ohta, M., Lee, M. & Mills, D. A. Indigenous bacteria and fungi drive traditional Kimoto sake fermentations. Appl. Environ. Microbiol. 80, 5522–5529 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Alexa, E. A. et al. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. Microbiome 12, 78 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hutkins, R. Microbiology and Technology of Fermented Foods 2nd edn (Wiley-Blackwell, 2018).

Wolfe, B. E. & Dutton, R. J. Fermented foods as experimentally tractable microbial ecosystems. Cell 161, 49–55 (2015).

Article  CAS  PubMed  Google Scholar 

Gänzle, M. G. et al. Starter culture development and innovation for novel fermented foods. Annu. Rev. Food Sci. Technol. 15, 211–239 (2024).

Article  PubMed  Google Scholar 

Johansen, E. Use of natural selection and evolution to develop new starter cultures for fermented foods. Annu. Rev. Food Sci. Technol. 9, 411–428 (2018).

Article  CAS  PubMed  Google Scholar 

Wolfe, B. E., Button, J. E., Santarelli, M. & Dutton, R. J. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158, 422–433 (2014). Early example of the use of in vitro studies to gain mechanistic insights into microbial interactions important for cheese ripening.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rousseau, G. M. & Moineau, S. Evolution of Lactococcus lactis phages within a cheese factory. Appl. Environ. Microbiol. 75, 5336–5344 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spus, M. et al. Strain diversity and phage resistance in complex dairy starter cultures. J. Dairy Res. 98, 5173–5182 (2015). Characterization of the role of bacteriophage predation in community stability and function during the production of Gouda cheese.

CAS  Google Scholar 

Karahadian, C. & Lindsay, R. C. Integrated roles of lactate, ammonia, and calcium in texture development of mold surface-ripened cheese. J. Dairy Sci. 70, 909–918 (1987).

Article  CAS  Google Scholar 

Galli, B. D., Martin, J. G. P., da Silva, P. P. M., Porto, E. & Spoto, M. H. F. Sensory quality of Camembert-type cheese: relationship between starter cultures and ripening molds. Int. J. Food Microbiol. 234, 71–75 (2016). Study reporting on the interplay between moulds and lactic acid bacteria and their effects on cheese properties.

Article  CAS  PubMed  Google Scholar 

Gillot, G. et al. Functional diversity within the Penicillium roqueforti species. Int. J. Food Microbiol. 241, 141–150 (2017).

Article  CAS  PubMed  Google Scholar 

Caron, T. et al. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int. J. Food Microbiol. 354, 109174 (2021).

Article  CAS  PubMed  Google Scholar 

Dalzini, E. et al. Listeria monocytogenes in Gorgonzola cheese: study of the behavior throughout the process and growth predictioni during shelf life. Int. J. Food Microbiol. 262, 71–79 (2017).

Article  CAS  PubMed  Google Scholar 

Irlinger, F., Layec, S., Hélinck, S. & Dugat-Bony, E. Cheese rind microbial communities: diversity, composition and origin. FEMS Microbiol. Lett. 362, 1–11 (2015).

Article  CAS  PubMed  Google Scholar 

Gori, K., Sørensen, L. M., Petersen, M. A., Jespersen, L. & Arneborg, N. Debaryomyces hansenii strains differ in their production of flavor compounds in a cheese-surface model. MicrobiologyOpen 1, 161–168 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Decadt, H., Vermote, L., Díaz-Muñoz, C., Weckx, S. & De Vuyst, L. Decarboxylase activity of the non-starter lactic acid bacterium Loigolactobacillus rennini gives crack defects in Gouda cheese through the production of γ-aminobutyric acid. Appl. Environ. Microbiol. 90, e0165523 (2024).

Article  PubMed  Google Scholar 

Jayabalan, R., Malbaša, R. V., Lončar, E. S., Vitas, J. S. & Sathishkumar, M. A review on kombucha tea — microbiology, composition, fermentation, beneficial effects, toxicity, and tea fungus. Compr. Rev. Food Sci. Food Saf. 13, 538–550 (2014).

Article  PubMed  Google Scholar 

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