Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing

Abstract

Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the 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. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.

Figure 1

Illustration of read abundance with different functional hit category. (A) KEGG annotation (B) COGs and NOGs annotation and (C) Sub-system annotation.

Figure 2

KEGG pathway analysis from shotgun sequence data of keem through SRplot.

Figure 3

The most abundant population at different taxonomic levels in the keem sample (A) domain, (B) phylum, (C) class and (D) genus level.

Figure 4

Krona plot (A) and Sankey visualization (B) of bacterial diversity identified in keem.

Figure 5

Krona plot (A) and Sankey visualization (B) of archaeal diversity identified in keem.

Figure 6

Sankey plot/visualization showing the taxonomic distribution of fungal diversity found in keem.

Figure 7

Sankey plot/visualization showing the taxonomic distribution of viral diversity found in keem.