Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics

Grep-chhurpi, peha, peron namsing and perun similar to yaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPRCas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and perun similar to yaan with that of other fermented soybean foods of Asia revealed a distinct difference.

Automated summary

This study investigated the microbiome, metabolites, and metagenome-assembled genomes (MAGs) of four fermented soybean foods made by the native people of Arunachal Pradesh. The study found that bacteria dominated the microbiome, with lactobacilli being the most abundant. The metabolomics analysis revealed targeted and untargeted metabolites involved in flavor development and therapeutic properties. High-quality MAGs of certain species showed biomarkers associated with various bio-functional properties. The study also provided insights into the cultivability of these MAGs for future use as starter cultures in fermented soybean food production. Additionally, a comparison with other fermented soybean foods in Asia showed distinct differences in microbiome and metabolites.