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

Edoardo Pasolli,Paul D Cotter,Fabio Cumbo,Aaron M Walsh,John Leech,Danilo Ercolini,Nicola Segata,Italia E Mauriello,Francesca De Filippis

doi: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.

Highlights

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics
These represented mainly species of potential food origin, including bacteria occurring in probiotic supplements, in addition to typically non-food origin species such as Lactobacillus mucosae, Lactobacillus ruminis, and Lactobacillus salivarius (Fig. 1)
The two most prevalent species in the gut were Streptococcus thermophilus and Lactococcus lactis (16.3%), both commonly found in dairy products (Fig. 1, Supplementary Fig. 1, and Supplementary Data 3)

Summary

Introduction

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. LAB are regarded as components of the transient gut microbial community, coming from the external environment and with food representing the main source, which interacts daily with the longer term members of the gut microbiome[7] Despite this general view, it is still not known to what extent components of the food microbiome are actively transferred to become part of the gut microbiome and what role they play in this complex environment. We perform a large-scale genome-wide analysis of publicly available and newly sequenced food and human metagenomes to investigate the prevalence and diversity of LAB species with a view to identifying links between gut and food microbiomes. Comparative genomics suggest an overall food origin for the gut strains

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