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

Putatively health-associated foods, including fermented foods, have been the focus of ever greater interest. As the mechanisms via which the microbes in fermented foods have the potential to improve health are often not fully understood, it is necessary to develop a greater understanding of the composition and functionality of the fermented food microbiota in order 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, proved to be the primary driver of microbial composition with dairy foods found to have the lowest alpha diversity. From the combined dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Lactobacillus, Leuconostoc and Rouxiella, were generated. Potential health promoting attributes were explored and a number of foods, including waterkefirs, sauerkrauts and kvasses, were found to contain greater numbers of potentially health-associated gene clusters (PHAGCs), such as those responsible for colonisation and survival. Ultimately, this study provides a comprehensive insight into the microbiomes of fermented foods, the species that dominate and the PHAGCs and other attributes encoded by these microbes.