Cited by 203Gut microbiota and healthProbiotics and Fermented FoodsNutritional Studies and Diet

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Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

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Taylor, Bryn C., Lejzerowicz, Franck, Poirel, Marion, Shaffer, Justin P., Jiang, Lingjing, Aksenov, Alexander, Litwin, Nicole, Humphrey, Gregory, Martino, Cameron, Miller-Montgomery, Sandrine, Dorrestein, Pieter C., Veiga, Patrick, Song, Se Jin, McDonald, Daniel, Derrien, Muriel, Knight, Rob·2020·mSystems

DOI 10.1128/msystems.00901-19PMC PMC7380580

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Abstract

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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A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
Self-citation
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
Individual Comparisons by Ranking Methods
Wilcoxon, F. (1945) · Biometrics Bulletin · doi:10.2307/3001968 · Cited by 15,354
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Self-citation
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513
Self-citation
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357

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Centers for Disease Control and Prevention. 2018. National Health and Nutrition Examination Survey data, 2011–2012. Centers for Disease Control and Prevention, Atlanta, GA.
10.1128/mSystems.00031-18 · DOI · Paper page
Jiang L, Vazquez-Baeza Y, Gonzalez A, Natarajan L, Knight R, Thompson WK. 2019. Bayesian sparse functional principal components analysis models dynamic temporal changes in longitudinal microbiome studies, 1836–1853. In JSM Proceedings, Statistics in Epidemiology Section. American Statistical Association, Alexandria, VA. https://ww2.amstat.org/membersonly/proceedings/2019/data/assets/pdf/1199578.pdf.

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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: Taylor, Bryn C.
Lejzerowicz, Franck
Shaffer, Justin P.
Jiang, Lingjing
Aksenov, Alexander
Litwin, Nicole
Humphrey, Gregory
Martino, Cameron
Dorrestein, Pieter C.
Veiga, Patrick
Song, Se Jin
McDonald, Daniel
Derrien, Muriel
Knight, Rob
Venue: mSystems
Publisher: American Society for Microbiology
Published: 2020-04-28
Volume: 5
Issue: 2
ISSN: 2379-5077 (ISSN-L)
DOI: 10.1128/msystems.00901-19
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: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
journals.asm.org/non-commercial-tdm-license (tdm)
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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Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

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