Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

Abstract

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps 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 and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. 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. IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

Metagenomic Analysis of Bacterial Diversity in Traditional Fermented Foods Reveals Food-Specific Dominance of Specific Bacterial Taxa

“…These results suggest that the type of raw food material and the fermentation environment in these regions may impact bacterial richness but not the diversity. Similar findings have been previously reported in other types of fermented food products [51][52][53].…”

Microorganisms in Whole Botanical Fermented Foods Survive Processing and Simulated Digestion to Affect Gut Microbiota Composition

“…LAB strains extracted from sauerkraut have been shown to adhere to CaCo-2 cells and exert antibacterial activity against potential pathogens ( Beganović et al, 2014 ). Leech et al (2020) recently found that the microbial diversity of tibicos and sauerkraut far exceeded that of dairy-based ferments, as well as containing the largest numbers of potential health-promoting gene clusters. As such, tibicos, and sauerkraut were chosen for our study.…”

Cell Surface Polysaccharides Represent a Common Strategy for Adsorption among Phages Infecting Lactic Acid Bacteria: Lessons from Dairy Lactococci and Streptococci

“…A holistic view of the biodiversity of bacterial and phage species of fermented foods is now achievable through a combination of metagenomic and virome analyses. Recently, metagenomic analysis of a range of fermented foods established that the substrate type is a major driver of the ecological diversity ( 14 ), which in turn will impact the phage population composition and dynamics. Virome studies of fermented foods are limited to date and represent a promising and informative alternative/complement to traditional phage screening studies to uncover the full extent of phage biodiversity and the emergence of novel phage species that may threaten food production systems ( Fig.…”