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Gigascience. 2019 Mar 1;8(3). pii: giz004. doi: 10.1093/gigascience/giz004.

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

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Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India.
Department of Genomic Science, Central University of Kerala, Periye Post, Kasargod, Kerala, 671316, India.
Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, Kansas, KS 66506, USA.
Microbiomics Laboratory, Department of Animal Science, University of Minnesota, 1988 Fitch Avenue, Minnesota, MN 55108, USA.
Animal Disease Research & Diagnostic Laboratory, Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, South Dakota, SD 57007, USA.
Department of Anthropology, Northwestern University, 1810 Hinman Avenue, Evanston, Illinois, IL 60208, USA.



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.


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.


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.


Indian gut microbiome; branched chain amino acids; core gut microbiome; integrated gene catalog; metabolomics; metagenome-wide association study; metagenomics; short chain fatty acids; whole-genome shotgun

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