Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome
Open accessAbstract
Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.
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Early evidence indicates dietary microbes can become human microbiome members.
“and early evidence of dietary microbes becoming human microbiome members motivates a more comprehensive investigation of this phenomenon across food types and human populations. 44-47”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [45]
Whether food microbes detected in the human gut are indeed colonizers or simply transient requires further investigation.
“Moreover, whether food microbes detected in the humangutareindeed microbiome colonizers or simply transient requires further investigation. 45”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [45]
LAB play a vital role in dairy and are commonly found in the human gut.
“which play a vital role in dairy-the most sampled category-and are commonly found in the human gut.”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [45]
F. sanfranciscensis is otherwise very rarely found in gut metagenomes of westernized and non-westernized communities.
“a species otherwise very rarely found in gut metagenomes of westernized and non-westernized communities.56”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [56]
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- Authors
- Pasolli, E., De Filippis, F., Mauriello, I. E., Cumbo, F., Walsh, A. M., Leech, J., Cotter, P. D., Segata, N., & Ercolini, D.
- Affiliations
- University of Naples Federico II (IT)
- University of Trento (IT)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Corresponding author
- Ercolini, Danilo
- ORCID
- Venue
- Nature Communications
- Published
- 2020-05-25
- Volume
- 11
- Issue
- 1
- Pages
- 2610-2610
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7248083
- OpenAlex
- W3027854790
- Cited by
- 367
- References
- 67
- Citations by year
- 2026: 41 · 2025: 59 · 2024: 49 · 2023: 78 · 2022: 74 · 2021: 51 · 2020: 14 · 2019: 1
- FWCI
- 4.75
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Arrow@dit (Dublin Institute of Technology) (acceptedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by)
- T-Stór (Teagasc) (submittedVersion, cc-by-nc-sa)
- Lenus, The Irish Health Repository (Dr Steevens Hospital Library) (submittedVersion)
- Funders
- Joint Programming Initiative A healthy diet for a healthy life
- European Commission (HORIZON2020, 818368)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- lactic acid bacteria, gut microbiota, fermented foods, probiotics, metagenome-assembled genomes, Streptococcus thermophilus, Lactococcus lactis, human gut metagenome
- MeSH terms
- Gastrointestinal Microbiome, Fermented Foods, Animals, Food Microbiology, Humans, Life Style, Primates, Lactococcus lactis, Probiotics, Databases, Genetic, Streptococcus thermophilus, Metagenome, Lactobacillales
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