Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

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...

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Bibliographic Details
Published in:	Nature communications Vol. 11; no. 1; pp. 2610 - 12
Main Authors:	Pasolli, Edoardo, De Filippis, Francesca, Mauriello, Italia E., Cumbo, Fabio, Walsh, Aaron M., Leech, John, Cotter, Paul D., Segata, Nicola, Ercolini, Danilo
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 25-05-2020 Nature Publishing Group Nature Portfolio
Subjects:	49/23 631/158 631/326 631/326/2565 Animals Astrophysics Bacteria Comparative analysis Databases, Genetic Digestive system Fermented food Fermented Foods and Beverages - microbiology Food Food Microbiology Food sources Gastrointestinal Microbiome - genetics Genomes Geography Humanities and Social Sciences Humans Intestinal microflora Lactic acid Lactic acid bacteria Lactobacillales - genetics Lactobacillales - isolation & purification Lactococcus lactis - genetics Lactococcus lactis - isolation & purification Life Style Metagenome Microbiomes Microbiota multidisciplinary Physics Primates - microbiology Probiotics Science Science (multidisciplinary) Strains (organisms) Streptococcus thermophilus - genetics Streptococcus thermophilus - isolation & purification
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Summary:	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. Here, Pasolli et al. perform a large-scale genome-wide comparative analysis of publicly available and newly sequenced food and human metagenomes to investigate the prevalence and diversity of lactic acid bacteria (LAB), indicating food as a major source of LAB species in the human gut.
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-020-16438-8