Fermented food metagenomics reveals substrate-associated differences in taxonomy, health-associated- and antibiotic resistance-determinants

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that the consumption of these foods that help to address the negative consequences of ‘industrialization’ of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented food microbiota to better harness desirable traits. Here we considerably expand the understanding of fermented food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity and functional potential (including antimicrobial resistance, carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from around the Globe. Food type, i.e., dairy-, sugar- or brine-type fermented foods, was to be the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of and , were generated. Potential health promoting attributes were more common in fermented foods than non-fermented equivalents, with waterkefirs, sauerkrauts and kvasses containing the greatest numbers of potentially health-associated gene clusters (PHAGCs). Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date, and yields novel information regarding their relative health-promoting potential.