Fermented Foods as Experimentally Tractable Microbial Ecosystems

Diet rapidly and reproducibly alters the human gut microbiome

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Topographical and Temporal Diversity of the Human Skin Microbiome

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Community structure and metabolism through reconstruction of microbial genomes from the environment

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Patterns and Processes of Microbial Community Assembly

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Global patterns in bacterial diversity

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WHAT IS THE OBSERVED RELATIONSHIP BETWEEN SPECIES RICHNESS AND PRODUCTIVITY?

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Beyond biogeographic patterns: processes shaping the microbial landscape

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The Application of Ecological Theory Toward an Understanding of the Human Microbiome

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Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

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Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

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Traditional Cheeses: Rich and Diverse Microbiota with Associated Benefits

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Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

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Controlled mixed culture fermentation: a new perspective on the use of non- Saccharomyces yeasts in winemaking

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Synthetic microbial communities

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The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

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Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

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Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples

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Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

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Microbiology and Technology of Fermented Foods

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Species Interactions Alter Evolutionary Responses to a Novel Environment

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Big questions, small worlds: microbial model systems in ecology

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Unraveling Microbial Interactions in Food Fermentations: from Classical to Genomics Approaches

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Imaging mass spectrometry in microbiology

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Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

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Phylogenetic relatedness predicts priority effects in nectar yeast communities

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Taming Wild Yeast: Potential of Conventional and Nonconventional Yeasts in Industrial Fermentations

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Ecological parameters influencing microbial diversity and stability of traditional sourdough

Minervini, F., Angelis, M. D., Cagno, R. D., & Gobbetti, M. (2013) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2013.11.021 · Cited by 273 · see citing works

Microbial Interactions within a Cheese Microbial Community

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Niche engineering demonstrates a latent capacity for fungal-algal mutualism

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Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

Marsh, A. J., O’Sullivan, Ó., Hill, C., Ross, R. P., & Cotter, P. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069371 · Cited by 221 · see citing works

DNA Fingerprinting of Lactic Acid Bacteria in Sauerkraut Fermentations

Plengvidhya, V., Breidt, F., Lu, Z., & Fleming, H. P. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01342-07 · Cited by 214 · see citing works

Functional genomics of lactic acid bacteria: from food to health

Douillard, F. P., & de Vos, W. M. (2014) · Microbial Cell Factories · doi:10.1186/1475-2859-13-s1-s8 · Cited by 209 · see citing works

The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae

Gibbons, J. G., Salichos, L., Slot, J. C., Rinker, D. C., McGary, K. L., King, J. G., Klich, M. A., Tabb, D. L., McDonald, W. H., & Rokas, A. (2012) · Current Biology · doi:10.1016/j.cub.2012.05.033 · Cited by 202 · see citing works

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

Cheeseman, K., Ropars, J., Renault, P., Dupont, J., Gouzy, J., Branca, A., Abraham, A., Ceppi, M., Conseiller, E., Debuchy, R., et al. (2014) · Nature Communications · doi:10.1038/ncomms3876 · Cited by 198 · see citing works

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

Bokulich, N. A., Bamforth, C. W., & Mills, D. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035507 · Cited by 197 · see citing works

Molecular ecology and polyphasic characterization of the microbiota associated with semi-dry processed coffee (Coffea arabica L.)

Vilela, D. M., Pereira, G. V. D. M., Silva, C. F., Batista, L. R., & Schwan, R. F. (2010) · Food Microbiology · doi:10.1016/j.fm.2010.07.024 · Cited by 172 · see citing works

Microbial domestication signatures of <i>Lactococcus lactis</i> can be reproduced by experimental evolution

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Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives

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Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

Fierer, N., Barberán, A., & Laughlin, D. C. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00614 · Cited by 139 · see citing works

Biodiversity and dynamics of meat fermentations: The contribution of molecular methods for a better comprehension of a complex ecosystem

Cocolin, L., Dolci, P., & Rantsiou, K. (2011) · Meat Science · doi:10.1016/j.meatsci.2011.04.011 · Cited by 128 · see citing works

Next-generation approaches to the microbial ecology of food fermentations

Bokulich, N. A., & Mills, D. A. (2012) · BMB Reports · doi:10.5483/bmbrep.2012.45.7.148 · Cited by 122 · see citing works

Bioactive components in milk

German, J. B., Dillard, C. J., & Ward, R. E. (2002) · Current Opinion in Clinical Nutrition & Metabolic Care · doi:10.1097/00075197-200211000-00007 · Cited by 119 · see citing works

Indigenous Bacteria and Fungi Drive Traditional Kimoto Sake Fermentations

Bokulich, N. A., Ohta, M., Lee, M., & Mills, D. A. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00663-14 · Cited by 113 · see citing works

Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

Meersman, E., Steensels, J., Mathawan, M., Wittocx, P.-J., Saels, V., Struyf, N., Bernaert, H., Vrancken, G., & Verstrepen, K. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081559 · Cited by 104 · see citing works

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment

Celiker, H., & Gore, J. (2014) · Nature Communications · doi:10.1038/ncomms5643 · Cited by 86 · see citing works

Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation

Knight, S. J., & Goddard, M. R. (2014) · The ISME Journal · doi:10.1038/ismej.2014.132 · Cited by 84 · see citing works

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Almeida, M., Hébert, A., Abraham, A., Rasmussen, S., Monnet, C., Pons, N., Delbès, C., Loux, V., Batto, J.-M., Léonard, P., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1101 · Cited by 80 · see citing works

Genomic Evolution of Domesticated Microorganisms

Douglas, G. L., & Klaenhammer, T. R. (2010) · Annual Review of Food Science and Technology · doi:10.1146/annurev.food.102308.124134 · Cited by 70 · see citing works

Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron

Monnet, C., Back, A., & Irlinger, F. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.00085-12 · Cited by 59 · see citing works

Genotype-phenotype matching analysis of 38 Lactococcus lactisstrains using random forest methods

Bayjanov, J. R., Starrenburg, M. J. C., van der Sijde, M. R., Siezen, R. J., & van Hijum, S. A. F. T. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-68 · Cited by 37 · see citing works

Effect of Lineage-Specific Metabolic Traits of Lactobacillus reuteri on Sourdough Microbial Ecology

Lin, X. B., & Gänzle, M. G. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01783-14 · Cited by 34 · see citing works

The international scientific association for probiotics and prebiotics (ISAPP) consensus statement on fermented foods

Marco, M. L., Sanders, M. E., Gänzle, M., Arrieta, M. C., Cotter, P. D., De Vuyst, L., Hill, C., Holzapfel, W., Lebeer, S., Merenstein, D., et al. (2021) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/s41575-020-00390-5 · Cited by 937 · see citing works

Bacterial–fungal interactions: ecology, mechanisms and challenges

Deveau, A., Bonito, G. M., Uehling, J., Paoletti, M., Becker, M., Bindschedler, S., Hacquard, S., Hervé, V., Labbé, J., Lastovetsky, O. A., et al. (2018) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuy008 · Cited by 790 · see citing works

Challenges in microbial ecology: building predictive understanding of community function and dynamics

Stefanie Widder, A., Allen, R. J., Pfeiffer, T., Curtis, T. P., Wiuf, C., Sloan, W. T., Cordero, O. X., Brown, S. P., Momeni, B., Shou, W., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.45 · Cited by 742 · see citing works

Mystery behind Chinese liquor fermentation

Jin, G., Zhu, Y., & Xu, Y. (2017) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2017.02.016 · Cited by 714 · see citing works

Fermented foods in a global age: east meets West

Tamang, J. P., Cotter, P. D., Endo, A., Han, N. S., Kort, R., Liu, S. Q., Mayo, B., Westerik, N., & Hutkins, R. (2020) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12520 · Cited by 719 · see citing works

Understanding Kombucha Tea Fermentation: A Review

Villarreal‐Soto, S. A., Beaufort, S., Bouajila, J., Souchard, J., & Taillandier, P. (2018) · Journal of Food Science · doi:10.1111/1750-3841.14068 · Cited by 748 · see citing works

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

Walsh, A. M., Crispie, F., Kilcawley, K. N., O’Sullivan, Ó., O’Sullivan, M. G., Claesson, M. J., & Cotter, P. D. (2016) · mSystems · doi:10.1128/msystems.00052-16 · Cited by 352 · see citing works

Functional role of yeasts, lactic acid bacteria and acetic acid bacteria in cocoa fermentation processes

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Metabolic interactions in microbial communities: untangling the Gordian knot

Ponomarova, O., & Patil, K. R. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.06.014 · Cited by 268 · see citing works

Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu

Xiao, C., Lu, Z., Zhang, X., Wang, S., Ao, L., Shen, C., Shi, J., & Xu, Z. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01550-17 · Cited by 258 · see citing works

Metagenomics insights into food fermentations

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Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients

Vuyst, L. D., Comasio, A., & Kerrebroeck, S. V. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1976100 · Cited by 242 · see citing works

Synthetic Ecology of Microbes: Mathematical Models and Applications

Zomorrodi, A. R., & Segrè, D. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.10.019 · Cited by 212 · see citing works

Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

Zou, W., Zhao, C., & Luo, H. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00671 · Cited by 217 · see citing works

Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods

Wang, Y., Zhang, C., Liu, F., Jin, Z., & Xia, X. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.2025035 · Cited by 220 · see citing works

Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants

Leech, J., Cabrera-Rubio, R., Walsh, A. M., Macori, G., Walsh, C. J., Barton, W., Finnegan, L., Crispie, F., O’Sullivan, O., Claesson, M. J., et al. (2020) · mSystems · doi:10.1128/msystems.00522-20 · Cited by 200 · see citing works

Traditional low-alcoholic and non-alcoholic fermented beverages consumed in European countries: a neglected food group

Baschali, A., Tsakalidou, E., Kyriacou, A., Karavasiloglou, N., & Matalas, A. (2017) · Nutrition Research Reviews · doi:10.1017/s0954422416000202 · Cited by 204 · see citing works

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., & Ercolini, D. (2016) · Scientific Reports · doi:10.1038/srep21871 · Cited by 196 · see citing works

Construction of Synthetic Microbiota for Reproducible Flavor Compound Metabolism in Chinese Light-Aroma-Type Liquor Produced by Solid-State Fermentation

Wang, S., Wu, Q. J., Nie, Y., Wu, J., & Xu, Y. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.03090-18 · Cited by 185 · see citing works

Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem

May, A., Narayanan, S., Alcock, J., Varsani, A., Maley, C. C., & Aktipis, A. (2019) · PeerJ · doi:10.7717/peerj.7565 · Cited by 189 · see citing works

Review article: the future of microbiome‐based therapeutics

Gulliver, E. L., Young, R. B., Chonwerawong, M., D’Adamo, G. L., Thomason, T., Widdop, J. T., Rutten, E. L., Marcelino, V. R., Bryant, R. V., Costello, S. P., et al. (2022) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.17049 · Cited by 192 · see citing works

Dietary short-chain fatty acid intake improves the hepatic metabolic condition via FFAR3

Shimizu, H., Masujima, Y., Ushiroda, C., Mizushima, R., Taira, S., Ohue‐Kitano, R., & Kimura, I. (2019) · Scientific Reports · doi:10.1038/s41598-019-53242-x · Cited by 184 · see citing works

Microbial Dynamics between Yeasts and Acetic Acid Bacteria in Kombucha: Impacts on the Chemical Composition of the Beverage

Tran, T., Grandvalet, C., Verdier, F., Martin, A., Alexandre, H., & Tourdot‐Maréchal, R. (2020) · Foods · doi:10.3390/foods9070963 · Cited by 175 · see citing works

Recent Past, Present, and Future of the Food Microbiome

De Filippis, F., Parente, E., & Ercolini, D. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012312 · Cited by 163 · see citing works

Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea

Zhao, M., Su, X. Q., Nian, B., Chen, L. J., Zhang, D. L., Duan, S., Wang, L. Y., Shi, X., Jiang, B., Jiang, W., et al. (2019) · mSystems · doi:10.1128/msystems.00680-19 · Cited by 163 · see citing works

Inhibitory Effect of Lactic Acid Bacteria on Foodborne Pathogens: A Review

Gao, Z., Daliri, E. B., Wang, J., Liu, D., Chen, S., Ye, X., & Ding, T. (2019) · Journal of Food Protection · doi:10.4315/0362-028x.jfp-18-303 · Cited by 159 · see citing works

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation

Pang, X., Han, B., Huang, X., Zhang, X., Hou, L.-F., Cao, M., Gao, L., Hu, G., & Chen, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-21814-y · Cited by 154 · see citing works

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes

Zhang, Y., Kastman, E. K., Guasto, J., & Wolfe, B. E. (2018) · Nature Communications · doi:10.1038/s41467-017-02522-z · Cited by 153 · see citing works

Drivers that establish and assembly the lactic acid bacteria biota in cheeses.

Gobbetti, M., Di Cagno, R., Calasso, M., Neviani, E., Fox, P. F., & De Angelis, M. (2018) · Trends in Food Science &amp; Technology · doi:10.1016/j.tifs.2018.06.010 · Cited by 151 · see citing works

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Mannaa, M., Han, G., Seo, Y., & Park, I. (2021) · Foods · doi:10.3390/foods10112861 · Cited by 160 · see citing works

Gut Microbiota-Derived Short-Chain Fatty Acids Facilitate Microbiota:Host Cross talk and Modulate Obesity and Hypertension

Overby, H., & Ferguson, J. F. (2021) · Current Hypertension Reports · doi:10.1007/s11906-020-01125-2 · Cited by 153 · see citing works

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness

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The genomics of microbial domestication in the fermented food environment

Gibbons, J. G., & Rinker, D. C. (2015) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.07.003 · Cited by 142 · see citing works

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

Marsland, R., Cui, W., Goldford, J. E., Sánchez, Á., Korolev, K. S., & Mehta, P. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006793 · Cited by 141 · see citing works

Metagenomic insights into the dynamics of microbial communities in food

Kergourlay, G., Taminiau, B., Daube, G., & Vergès, M.-C. C. (2015) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.09.010 · Cited by 139 · see citing works

The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies

Mantravadi, P. K., Kalesh, K., Dobson, R. C. J., Hudson, A. O., & Parthasarathy, A. (2019) · Antibiotics · doi:10.3390/antibiotics8010008 · Cited by 141 · see citing works

Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Lino, F. S. D. O., Bajić, D., Vila, J. C. C., Sánchez, Á., & Sommer, M. O. A. (2021) · Nature Communications · doi:10.1038/s41467-021-21844-7 · Cited by 136 · see citing works

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