Does consumption of fermented foods modify the human gut microbiota?
Open accessAbstract
The human microbiota is a key contributor to many aspects of human health and its composition is largely influenced by diet. There is a growing body of scientific evidence to suggest that gut dysbiosis (microbial imbalance of the intestine) is associated with inflammatory and immune-mediated diseases (e.g., inflammatory bowel disease and asthma). Regular consumption of fermented foods (e.g., kimchi, kefir, etc.) may represent a potential avenue to counter the proinflammatory effects of gut dysbiosis. However, an assessment of the available literature in this research area is lacking. Here we provide a critical review of current human intervention studies that analyzed the effect of fermented foods on the composition and/or function of the human gut microbiota. A total of 19 human intervention studies were identified that met this search criteria. In this review, we discuss evidence that consumption of fermented foods may modify the gut microbiota in humans. Further, there is cursory evidence to suggest that gut microbiota compositional changes mediate associations between fermented food consumption and human health outcomes. Although promising, there remains considerable heterogeneity in the human populations targeted in the intervention studies we identified. Larger longitudinal feeding studies with longer follow-up are necessary to confirm and enhance the current data. Further, future studies should consider analyzing microbiota function as a means to elucidate the mechanism linking fermented food consumption with human health. This review highlights methodologic considerations for intervention trials, emphasizing an expanse of research opportunities related to fermented food consumption in humans.
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Not enough data are available yet to make inferences on any specific microbial patterns associated with a particular fermented food.
“Despite these promising results, a recent literature review concluded that not enough data are available yet to make inferences on any specific microbial patterns associated with a particular fermented food (196).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [196]
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Hill (2014) · doi:10.1038/nrgastro.2014.66 · Cited by 9,592 · see citing works
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820 · see citing works
Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413 · see citing works
den Besten, G., van Eunen, K., Groen, A. K., Venema, K., Reijngoud, D.-J., & Bakker, B. M. (2013) · Journal of Lipid Research · doi:10.1194/jlr.r036012 · Cited by 5,048 · see citing works
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182 · see citing works
Colonic Health: Fermentation and Short Chain Fatty Acids
Wong, J. M. W., de Souza, R., Kendall, C. W. C., Emam, A., & Jenkins, D. J. A. (2006) · Journal of Clinical Gastroenterology · doi:10.1097/00004836-200603000-00015 · Cited by 2,739 · see citing works
Health benefits of fermented foods: Microbiota and beyond
Marco, M. L., Heeney, D., Binda, S., Cifelli, C. J., Cotter, P. D., Foligné, B., Gänzle, M., Kort, R., Pasin, G., Pihlanto, A., et al. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2016.11.010 · Cited by 1,674 · see citing works
Probiotic Mechanisms of Action
Bermúdez-Brito, M., Plaza‐Díaz, J., Muñoz‐Quezada, S., Gómez‐Llorente, C., & Gil, Á. (2012) · Annals of Nutrition and Metabolism · doi:10.1159/000342079 · Cited by 1,276 · see citing works
Consumption of fermented milk product with probiotic modulates brain activity
Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., Guyonnet, D., Legrain–Raspaud, S., Trotin, B., Naliboff, B., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.02.043 · Cited by 1,192 · see citing works
Hemarajata, P., & Versalovic, J. (2013) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x12459294 · Cited by 1,083 · see citing works
Genetic determinants of the gut microbiome in UK twins
Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.017 · Cited by 1,048 · see citing works
LeBlanc, J. G., Chain, F., Martín, R., Bermúdez‐Humarán, L. G., Courau, S., & Langella, P. (2017) · Microbial Cell Factories · doi:10.1186/s12934-017-0691-z · Cited by 881 · see citing works
Queipo-Ortuño, M. I., Boto-Ordóñez, M., Murri, M., Gomez-Zumaquero, J. M., Clemente-Postigo, M., Estruch, R., Cardona Diaz, F., Andrés-Lacueva, C., & Tinahones, F. J. (2012) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.111.027847 · Cited by 671 · see citing works
The Gut Microbiome Profile in Obesity: A Systematic Review
Castaner, O., Goday, A., Park, Y.-M., Lee, S.-H., Magkos, F., Shiow, S.-A. T. E., & Schröder, H. (2018) · International Journal of Endocrinology · doi:10.1155/2018/4095789 · Cited by 570 · see citing works
Kombucha tea fermentation: Microbial and biochemical dynamics
Chakravorty, S., Bhattacharya, S., Chatzinotas, A., Chakraborty, W., Bhattacharya, D., & Gachhui, R. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.12.015 · Cited by 533 · see citing works
Health Benefits of Kimchi (Korean Fermented Vegetables) as a Probiotic Food
Park, K., Jeong, J., Lee, Y.-E., & Daily, J. W. (2014) · Journal of Medicinal Food · doi:10.1089/jmf.2013.3083 · Cited by 471 · see citing works
The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir
Bourrie, B. C. T., Willing, B. P., & Cotter, P. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00647 · Cited by 449 · see citing works
The role of the microbiome for human health: From basic science to clinical applications
Mohajeri, M. H., Brummer, R. J. M., Rastall, R. A., Weersma, R. K., Harmsen, H. J. M., Faas, M., & Eggersdorfer, M. (2018) · European Journal of Nutrition · doi:10.1007/s00394-018-1703-4 · Cited by 440 · see citing works
Moreno‐Indias, I., Sánchez‐Alcoholado, L., Pérez‐Martínez, P., Andrés‐Lacueva, C., Cardona, F., Tinahones, F. J., & Queipo‐Ortuño, M. I. (2015) · Food & Function · doi:10.1039/c5fo00886g · Cited by 374 · see citing works
The Role of the Microbiome in the Developmental Origins of Health and Disease
Stiemsma, L. T., & Michels, K. B. (2018) · PEDIATRICS · doi:10.1542/peds.2017-2437 · Cited by 361 · see citing works
Self-citationLinares, D. M., Gómez, C., Renes, E., Fresno, J. M., Tornadijo, M. E., Ross, R. P., & Stanton, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00846 · Cited by 335 · see citing works
Coffee fermentation and flavor – An intricate and delicate relationship
Lee, L. W., Cheong, M. W., Curran, P., Yu, B., & Liu, S. (2015) · Food Chemistry · doi:10.1016/j.foodchem.2015.03.124 · Cited by 326 · see citing works
Kimchi and Other Widely Consumed Traditional Fermented Foods of Korea: A Review
Patra, J. K., Das, G., Paramithiotis, S., & Shin, H. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01493 · Cited by 320 · see citing works
Interindividual variability in gut microbiota and host response to dietary interventions
Healey, G. R., Murphy, R., Brough, L., Butts, C. A., & Coad, J. (2017) · Nutrition Reviews · doi:10.1093/nutrit/nux062 · Cited by 296 · see citing works
Arrieta, M., Arévalo‐Cortes, A., Stiemsma, L. T., Dimitriu, P. A., Chico, M. E., Loor, S., Vaca, M. G., Boutin, R. C. T., Morien, E., Jin, M., et al. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.08.041 · Cited by 277 · see citing works
Self-citationRole of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease
Martín, R., Miquel, S., Ulmer, J., Kechaou, N., Langella, P., & Bermúdez‐Humarán, L. G. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-71 · Cited by 269 · see citing works
Changes of the human gut microbiome induced by a fermented milk product
Veiga, P., Pons, N., Agrawal, A., Oozeer, R., Guyonnet, D., Brazeilles, R., Faurie, J., Vlieg, J. E. T. V. H., Houghton, L. A., Whorwell, P. J., et al. (2014) · Scientific Reports · doi:10.1038/srep06328 · Cited by 257 · see citing works
Impact of Coffee Consumption on the Gut Microbiota: A Human Volunteer Study
Jaquet, M., Rochat, I., Moulin, J., Cavin, C., & Bibiloni, R. (2009) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2009.01.011 · Cited by 232 · see citing works
Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition
Fulde, M., Sommer, F., Chassaing, B., van Vorst, K., Dupont, A., Hensel, M., Basic, M., Klopfleisch, R., Rosenstiel, P., Bleich, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0395-5 · Cited by 206 · see citing works
Yılmaz, İ., Dolar, M. E., & Özpınar, H. (2019) · Turkish Journal of Gastroenterology · doi:10.5152/tjg.2018.18227 · Cited by 193 · see citing works
Han, K., Bose, S., Wang, J., Kim, B., Kim, M. J., Kim, E., & Kim, H. (2015) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201400780 · Cited by 121 · see citing works
Tuohy, K. M., Finlay, R. K., Wynne, A. G., & Gibson, G. R. (2001) · Anaerobe · doi:10.1006/anae.2001.0368 · Cited by 120 · see citing works
Beneficial Effects of Fresh and Fermented Kimchi in Prediabetic Individuals
An, S.-Y., Lee, M. S., Jeon, J. Y., Ha, E. S., Kim, T. H., Yoon, J. Y., Ok, C.-O., Lee, H., Hwang, W., Choe, S. J., et al. (2013) · Annals of Nutrition and Metabolism · doi:10.1159/000353583 · Cited by 116 · see citing works
Yang, Y., & Sheu, B. (2012) · Helicobacter · doi:10.1111/j.1523-5378.2012.00941.x · Cited by 113 · see citing works
Nielsen, E. S., Garnås, E., Jensen, K. J., Hansen, L. H., Olsen, P. S., Ritz, C., Krych, L., & Nielsen, D. S. (2018) · Food & Function · doi:10.1039/c8fo00968f · Cited by 113 · see citing works
Beneficial properties of lactic acid bacteria naturally present in dairy production
Colombo, M., Castilho, N. P. A., Todorov, S. D., & Nero, L. A. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1356-8 · Cited by 113 · see citing works
Shadnoush, M., Hosseini, R. S., Khalilnezhad, A., Navai, L., Goudarzi, H., & Vaezjalali, M. (2015) · Korean Journal of Gastroenterology · doi:10.4166/kjg.2015.65.4.215 · Cited by 98 · see citing works
Foligné, B. (2010) · World Journal of Gastroenterology · doi:10.3748/wjg.v16.i17.2134 · Cited by 83 · see citing works
Effect of acute and chronic red wine consumption on lipopolysaccharide concentrations
Clemente‐Postigo, M., Queipo‐Ortuño, M. I., Boto‐Ordóñez, M., Coín‐Aragüez, L., Roca-Rodríguez, M. D. M., Delgado‐Lista, J., Cardona, F., Andrés‐Lacueva, C., & Tinahones, F. J. (2013) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.051128 · Cited by 81 · see citing works
Effects of Dietary Yogurt on the Healthy Human Gastrointestinal (GI) Microbiome
Lisko, D. J., Johnston, G. P., & Johnston, C. G. (2017) · Microorganisms · doi:10.3390/microorganisms5010006 · Cited by 80 · see citing works
Odamaki, T., Sugahara, H., Yonezawa, S., Yaeshima, T., Iwatsuki, K., Tanabe, S., Tominaga, T., Togashi, H., Benno, Y., & Xiao, J. (2011) · Anaerobe · doi:10.1016/j.anaerobe.2011.11.004 · Cited by 78 · see citing works
Changes in human gut microbiota influenced by probiotic fermented milk ingestion
Unno, T., Choi, J.-H., Hur, H.-G., Sadowsky, M. J., Ahn, Y., Huh, C., Kim, G.-B., & Cha, C. (2015) · Journal of Dairy Science · doi:10.3168/jds.2014-8943 · Cited by 77 · see citing works
Effect of fermented soy milk on the intestinal bacterial ecosystem
Cheng, I.-C. (2005) · World Journal of Gastroenterology · doi:10.3748/wjg.v11.i8.1225 · Cited by 75 · see citing works
Marzano, M., Fosso, B., Manzari, C., Grieco, F., Intranuovo, M., Cozzi, G., Mulè, G., Scioscia, G., Valiente, G., Tullo, A., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157383 · Cited by 73 · see citing works
Inoguchi, S., Ohashi, Y., Narai‐Kanayama, A., Aso, K., Nakagaki, T., & Fujisawa, T. (2011) · International Journal of Food Sciences and Nutrition · doi:10.3109/09637486.2011.630992 · Cited by 71 · see citing works
Phylogenetic profile of gut microbiota in healthy adults after moderate intake of red wine
Barroso, E., Muñoz‐González, I., Jiménez, E., Bartolomé, B., Moreno-Arribas, M. V., Peláez, C., Martínez‐Cuesta, M. C., & Requena, T. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600620 · Cited by 53 · see citing works
非工業化環境における幼児の真菌と細菌性赤痢と小児アトピー性喘鳴との関連性【JST・京大機械翻訳】
Arrieta, M., Andrea, A., Leah, S., Pedro, D., Martha, E. C., Loor, S., Vaca, M. G., Rozlyn, C. T. B., Evan, M., Mingliang, J., et al. (2018) · Journal of Allergy and Clinical Immunology · Cited by 44 · see citing works
Dairy intake in relation to breast and pubertal development in Chilean girls,
Gaskins, A. J., Pereira, A. P. R., Quintiliano, D. A., Shepherd, J., Uauy, R. D., Corvalán, C., & Michels, K. B. (2017) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.116.150359 · Cited by 42 · see citing works
Self-citationLactic acid bacteria mediated fermented soybean as a potent nutraceutical candidate
Sirilun, S., Sivamaruthi, B. S., Kesika, P., et al. (2017) · Asian Pacific Journal of Tropical Biomedicine · doi:10.1016/j.apjtb.2017.09.007 · Cited by 39 · see citing works
Ai, C., Ma, N., Zhang, Q.-X., Wang, G., Liu, X., Tian, F., Chen, P., & Chen, W. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164697 · Cited by 38 · see citing works
Grieco, F., Carluccio, M. A., & Giovinazzo, G. (2019) · Foods · doi:10.3390/foods8100453 · Cited by 31 · see citing works
Lay, C., Sutren, M., Lepercq, P., Juste, C., Rigottier‐Gois, L., Lhoste, E. F., Lemée, R., Ruyet, P. L., Dore, J. M., & Andrieux, C. (2004) · British Journal Of Nutrition · doi:10.1079/bjn20041192 · Cited by 30 · see citing works
Firmesse, O., Alvaro, E., Mogenet, A., Bresson, J., Lemée, R., Ruyet, P. L., Bonhomme, C., Lambert, D., Andrieux, C., Dore, J. M., et al. (2008) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2008.03.044 · Cited by 30 · see citing works
Chiu, H., Chen, Y., Lu, Y., et al. (2016) · Journal of Food and Drug Analysis · doi:10.1016/j.jfda.2016.10.008 · Cited by 29 · see citing works
Impact of Saccharomyces cerevisiae Strains on Health-Promoting Compounds in Wine
Guerrini, S., Mangani, S., Romboli, Y., Luti, S., Pazzagli, L., & Granchi, L. (2018) · Fermentation · doi:10.3390/fermentation4020026 · Cited by 26 · see citing works
Firmesse, O., Rabot, S., Bermúdez‐Humarán, L. G., et al. (2007) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2007.00933.x · Cited by 25 · see citing works
Yamamoto, B., Suzuki, Y., Yonezu, T., et al. (2018) · Bioscience Biotechnology and Biochemistry · doi:10.1080/09168451.2018.1443789 · Cited by 14 · see citing works
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- Authors
- Stiemsma, L. T., Nakamura, R. E., Nguyen, J. G., & Michels, K. B.
- Affiliations
- University of California, Los Angeles (US)
- University of Freiburg (DE)
- Corresponding author
- Michels, Karin B
- Venue
- The Journal of Nutrition
- Publisher
- Elsevier BV
- Published
- 2020-07
- Volume
- 150
- Issue
- 7
- Pages
- 1680-1692
- ISSN
- 0022-3166 (ISSN-L)
- PMC
- PMC7330458
- OpenAlex
- W3013188026
- Cited by
- 144
- References
- 58
- Citations by year
- 2026: 21 · 2025: 30 · 2024: 26 · 2023: 21 · 2022: 24 · 2021: 17 · 2020: 5
- FWCI
- 1.60
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Nutrition (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute
- National Institutes of Health (5T32CA009142-37)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- fermented foods, gut microbiota, gut dysbiosis, kimchi, kefir, dietary intervention, inflammatory bowel disease, asthma, microbiota function, diet and health, human intervention studies
- MeSH terms
- Gastrointestinal Microbiome, Fermented Foods, Bacteria, Humans
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