Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome
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Public interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented food consumers have subtle differences in their gut microbiota structure, which is enriched in conjugated linoleic acid, thought to be beneficial. The results suggest that further studies of specific kinds of fermented food and their impacts on the microbiome and health will be useful.
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People who consumed fermented plants 1 or 2 times per week or once per day had a dose-dependent, significantly different gut community measured by beta-diversity compared with nonconsumers.
“another recent study analyzing samples from 115 individuals in the American Gut Project showed that people who consumed fermented plants 1 or 2 times per week or once per day had a dosedependent, significantly different gut community measured by β-diversity compared with nonconsumers.”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [59]
An association between fermented food consumption and abundance of bacterial taxa as well as microbial functional profile was reported.
“Additionally, an association between fermented food consumption and abundance of bacterial taxa (e.g., Bacteroides, Pseudomonas, Dorea, Prevotella, Oscillospira, F. prausnitzii, Lactobacillus spp.) as well as microbial functional profile was reported (59).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [59]
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Fermented food consumption modulates the oral microbiota
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Li, Y., Fu, S., Klein, M. S., & Wang, H. (2024) · Microorganisms · doi:10.3390/microorganisms12071433 · Cited by 14 · see citing works
Patumcharoenpol, P., Nakphaichit, M., Panagiotou, G., Senavonge, A., Suratannon, N., & Vongsangnak, W. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008487 · Cited by 14 · see citing works
Plant-Based Fermented Foods: Classification, Biochemical Transformations, and Health Benefits
Peng, B., Nie, P., & Xu, H. (2025) · Fermentation · doi:10.3390/fermentation11070364 · Cited by 13 · see citing works
Guse, K., Sharma, A. K., Weyenberg, E., Davison, S., Ma, Y., Choi, Y., Johnson, A. J., Chen, C., & Gomez, A. M. (2023) · Gut Microbiome · doi:10.1017/gmb.2023.9 · Cited by 12 · see citing works
- Authors
- Taylor, B. C., Lejzerowicz, F., Poirel, M., Shaffer, J. P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., Dorrestein, P. C., Veiga, P., Song, S. J., McDonald, D., Derrien, M., & Knight, R.
- Affiliations
- University of California San Diego (US)
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Vlaams Instituut voor Biotechnologie (BE)
- Corresponding author
- Derrien, Muriel
- Knight, Rob
- ORCID
- Venue
- mSystems
- Publisher
- American Society for Microbiology
- Published
- 2020-04-28
- Volume
- 5
- Issue
- 2
- ISSN
- 2379-5077 (ISSN-L)
- PMC
- PMC7380580
- OpenAlex
- W3011493793
- Cited by
- 203
- References
- 74
- Citations by year
- 2026: 20 · 2025: 39 · 2024: 45 · 2023: 32 · 2022: 28 · 2021: 23 · 2020: 16
- FWCI
- 8.03
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mSystems (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Center for Research on Intelligent Storage and Processing in-memory
- Danone
- 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 › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
- Keywords
- fermented foods, gut microbiota, metabolome, conjugated linoleic acid, microbiota composition, dietary intake, human microbiome
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