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

Edoardo Pasolli, Francesca Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata and Danilo Ercolini ()
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Edoardo Pasolli: University of Naples Federico II
Francesca Filippis: University of Naples Federico II
Italia E. Mauriello: University of Naples Federico II
Fabio Cumbo: University of Trento
Aaron M. Walsh: Teagasc Food Research Centre
John Leech: Teagasc Food Research Centre
Paul D. Cotter: Teagasc Food Research Centre
Nicola Segata: University of Trento
Danilo Ercolini: University of Naples Federico II

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16438-8

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