Targeted amplicon sequencing reveals the probiotic potentials of microbial communities associated with traditional fermented foods of northeast India

Abstract

Ethnic fermented foods are being consumed from the ancient times with a belief of having health benefits and could serve as potential source of probiotics; but there is little understanding of the microorganisms performing the fermentation processes. Apart from these benefits occasional acquisition of pathogenic microorganisms may pose health risks. Further, most of the marketed probiotic strains generally are non-indigenous in nature, thus the efficacy in a population is questionable. Hence, the present study attempts to decipher the microbial communities associated with the ethnic fermented food from northeast part of India, using high throughput sequencing approach. We noted food specific enrichment of bacterial genera viz. Lactobacillus (90.7%) in ‘Axone’, Bacillus (62%) and Clostridium (15.9%) in ‘Bastenga’ and, Lactobacillus (47.8%) and Staphylococcus (36.3%) in ‘Chathur’, whereas Saccharomyces (98.7%) belonging to phylum Ascomycota predominates the fungal communities among all the samples. Assessment of probiotic potential inferred using PICRUSt2 suggests differential abundance of genes featuring active removal of stressors, cell envelope and cell surface proteins enabling gut survival by microbial communities. Interestingly, fungal communities showed difference prevalence of luxS gene catering anti-pathogenic effect. This, represents an opportunity to identify an indigenous probiotic candidate.