Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations

Abstract

Background Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we performed a large-scale and comprehensive investigation for the BGCs in global food fermentations by metagenomics analysis. Results We recovered 653 bacterial metagenome-assembled genomes (MAGs) from 367 metagenomic sequencing datasets covering 15 general food fermentation types worldwide. In total, 2334 secondary metabolite BGCs, including 1003 novel BGCs, were identified in these MAGs. Bacillaceae, Streptococcaceae, Streptomycetaceae, Brevibacteriaceae and Lactobacillaceae contained high abundances of novel BGCs (≥ 60 novel BGCs). Among 2334 BGCs, 1655 were habitat-specific, originating from habitat-specific species (80.54%) and habitat-specific genotypes within multi-habitat species (19.46%) in different food fermentation types. Biological activity analysis suggested that 183 BGC-producing secondary metabolites exhibited high probabilities of antibacterial activity (> 80%). These 183 BGCs were distributed across all 15 food fermentation types, and cheese fermentation contained the most BGC number. Conclusions This study demonstrates that food fermentation systems are an untapped reservoir of BGCs and bioactive secondary metabolites, and it provides novel insights into the potential human health benefits of fermented foods.

Microbial Antioxidants and Their Interactions with Gastrointestinal Tract Epithelial Cells in the Cattle

“…Moreover, within 167 types of natural products derived from 26,503 BGCs, a series of Betalactone (3,027 BGC products) and Arylpolyene (2,637 BGC products) were identi ed. Betalactone and Arylpolyene are recognized as substances involved in food fermentation and plant defense mechanisms 24 , with the potential of antioxidant, antibacterial, and anticancer activities. For the 1,031 completely novel BGCs, 15 distinct products categories, including 20% NRPS, 15.1% RRE-containing, 10.7% cyclic-lactone-autoinducer were encoded (Fig.…”