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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome
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2020-05-25
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Pasolli, E., De Filippis, F., Mauriello, I.E. et al. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun 11, 2610 (2020). https://doi.org/10.1038/s41467-020-16438-8
Abstract
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.