The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

Abstract

Background Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples. Results The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus , and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella . In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters. Conclusions The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.

Metagenomics analysis reveals features unique to Indian distal gut microbiota

“…A recent study by Dhakan et al [34] used multi-omics approaches to study samples from subjects of North-Central (Madhya Pradesh) and South (Kerala) India. Their study also indicated Prevotella as the dominant genus in North-Central India (where subjects mostly consumed a plant-based diet), whereas Bacteroides, Ruminococcus and Faecalibacterium were prominent in the gut microbiome of the cohort from Southern India (with a more omnivorous diet).…”

“…Several studies have previously been performed on Indian subjects, too, with their wide focus on healthy and malnourished children [27,28], lean, obese and surgically treated obese individuals of Indian origin [29], Mongoloid and Proto-Australoid tribal populations from North-East India and South India [30], healthy individuals from urban and rural areas of Delhi and Pune [31], healthy individuals from high altitude and low altitude regions [32], healthy individuals from Western India [33], Bhopal and Kerala [34] and tuberculosis patients from Delhi [35]. Albeit some of these reported studies of the Indian gut microbiota are metagenomics studies [27,28,34,35], most of them are taxonomic profiling studies performed using 16S rRNA gene sequencing. These studies indicate the presence of the phyla,…”

M-GWAS for the gut microbiome in Chinese adults illuminates on complex diseases

“…Unlike M-GWAS using chip data from European cohorts, we identified suggestive host genetic associations for the controversial concept of enterotypes (Fig. 1, Table S1D ), possibly due to higher prevalence of Prevotella in developing countries (Dhakan et al, 2019; Vangay et al, 2018). Principle coordinate analysis (PCoA) as well as Dirichlet multinominal mixture model using Bray-Curtis dissimilarity showed that this Chinese cohort could be formed into two clusters dominated by Bacteroides and Prevotella (Zou et al, 2019), containing 440 and 178 individuals, respectively (Fig.…”

Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model

“…Gut microbiome influences health and disease (1-3) and is highly affected by diet (4-6). Some of the dietary components are known to enhance host health by promoting the growth of beneficial bacteria in the gut, termed as “prebiotics” (7, 8).…”