Microbial community structure and functional gene analysis of Keem (a starter culture) native to Jaunsari tribe of Uttarakhand, India

Abstract

Abstract The present work describes the microbial community and gene function in the microbiome associated with Keem, a starter culture used by Jaunsari tribal community of India, for making various traditional alcoholic beverages. For this, Illumina based (MiSeq system) whole metagenome shotgun sequencing approach was followed after extraction of genomic DNA from the starter culture. Initially 22,350,940 sequences with an average base length of 151 bps were obtained comprising a total read of 3,374,991,940 bp. The genomic DNA of human and plant origin was separated during quality control (QC) check and not considered for subsequent downstream analysis. Post QC a total number of 8,665,213 sequences with 1,156,651,659 bp were analysed using MG-RAST which revealed the dominance of bacteria in the microbial community of Keem (95.81% sequences) followed by eukaryota (4.11%), archaea (0.05%) and virus (0.03%). At phylum level, Actinobacteria (81.18%) was the most abundant followed by Firmicutes (10.56%), Proteobacteria (4.00%) and Ascomycota (3.02%). The most predominant genus was Saccharopolyspora (36.31%) followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (875%), Bacillus (4.59%) and Brachybacterium (3.42%). At species level bacterial, fungal and virus population of Keem sample could be categorized into 3347, 57 and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem and KEGG Orthology (KO) annotations.