Molecular Characterization and Meta-Analysis of Gut Microbial Communities Illustrate Enrichment of Prevotella and Megasphaera in Indian Subjects

Abstract

The gut microbiome has varied impact on the wellbeing of humans. It is influenced by different factors such as age, dietary habits, socio-economic status, geographic location, and genetic makeup of individuals. For devising microbiome-based therapies, it is crucial to identify population specific features of the gut microbiome. Indian population is one of the most ethnically, culturally, and geographically diverse, but the gut microbiome features remain largely unknown. The present study describes gut microbial communities of healthy Indian subjects and compares it with the microbiota from other populations. Based on large differences in alpha diversity indices, abundance of 11 bacterial phyla and individual specific OTUs, we report inter-individual variations in gut microbial communities of these subjects. While the gut microbiome of Indians is different from that of Americans, it shared high similarity to individuals from the Indian subcontinent i.e., Bangladeshi. Distinctive feature of Indian gut microbiota is the predominance of genus Prevotella and Megasphaera. Further, when compared with other non-human primates, it appears that Indians share more OTUs with omnivorous mammals. Our metagenomic imputation indicates higher potential for glycan biosynthesis and xenobiotic metabolism in these subjects. Our study indicates urgent need of identification of population specific microbiome biomarkers of Indian subpopulations to have more holistic view of the Indian gut microbiome and its health implications.

Keywords: 16S rRNA amplicon; Indian subjects; Prevotella and Megasphaera; qPCR.

Figure 1

(A) Variation in alpha diversity indices in Indian Subjects. (B) Abundance of dominant bacterial phyla in Indian subjects. Subjects are separated and shown according to sequencing platform used. Samples with prefix PMS are from rural region and rest are from urban region. (C) Unweighted and (D) weighted UniFrac PCoA bi-plots; the gray colored sphere represent a taxonomic group that influence clustering of samples in particular area of the PCoA plot and its size demonstrate abundance of that taxonomic group (Rural samples are encircled). Colors indicate the sequencing technology used. Red: Illumina, Green: Ion Torrent PGM.

Figure 2

16S rRNA gene copy number of bacterial genera of most and least abundant bacterial OTUs in Indian subjects. The results are expressed as percent abundance of Prevotella, Faecalibacterium and Megasphaera to that of the total bacteria for each of the sample.

Figure 3

(A) Phylum level abundance of gut microbiota in Indians (green box) and Americans (red box), the boxes represent interquartile range (IQR), and the line between boxes indicate median value. (B) Abundance of significantly different bacterial families in Indians and Americans (Welch's t-test P-value below 0.05).

Figure 4

Principal coordinate analysis (PCoA) of UniFrac distance matrices; samples are colored according to the country (A,B) and according to the diet for comparison with non-human primates (C,D). (A) unweighted and (B) weighted UniFrac PCoA bi-plots; showing clustering of Indians and Americans, the gray colored sphere represent a taxonomic group that influence clustering of these samples in particular area of PCoA plot and its size demonstrate abundance of that taxonomic group. (C) Unweighted and (D) weighted UniFrac PCoA bi-plots; showing clustering of Indians and non-human primates.

Figure 5

(A) Family level distribution of bacterial taxa among: Indian, Bangladeshi, American, Korean, and Spanish population. (B) Venn diagram demonstrating overlap of OTUs at 97% sequence similarity cut off among these populations.

Figure 6

(A) Family level distribution of bacterial taxa among: Indians and non-human primates. (B) Venn diagram demonstrating overlap of OTUs at 97% sequence similarity cut off among Indians and non-human primates.

Figure 7

Metagenomic imputation. (A) Cladogram from LEfSe analysis representing differentially abundant KOs between Indians and Americans. (B) Visualization of unique metabolic functions among the Indians and other non-human primates.