The largest gut microbiome study of the Indian population reveals microbial composition is both region- and diet-specific

Microbiome studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health. However, most of these studies have been carried out in western countries and the Indian gut microbiome is not well explored. Since dietary habits and lifestyle play a key role in shaping the gut microbiome, large differences in the Indian gut microbiome compared with other populations are expected due to the country’s unique lifestyle and eating habits.

A study, guided by Dr. Vineet Sharma from the MetaBioSys Laboratory at the Indian Institute of Science Education and Research (IISER Bhopal, India), reports on initial insights into the unique structure and composition of the gut microbiome from the largest Indian cohort comprising 110 subjects. Previous findings by Dr Sharma’s group have also reported on the dysbiosis of the gut microbiome in diseases such as autism and tuberculosis. The group’s exploratory studies also analyzed scalp microflora in Indian subjects and established the role of scalp microbiome in scalp health.

The first extensive effort to reveal the compositions and functions of the gut microbiome in Indian individuals from the north and south of the country was published in the March 2019 issue of GigaScience. The multiomics study also correlated the microbiome composition with differences in dietary habits and geographical locations, and compared the Indian gut microbiome with nine other populations from around the world. The metagenomic and metabolomic characterization of fecal samples also revealed the signature microbial metabolites and genes specific to the two Indian cohorts.

The Unique Indian Gene catalogue: The study compared the 1.55 million microbial genes present in the Indian gut with the genes in the integrated gene catalogue (IGC, established by Qin et al. in 2010 and updated by Li et al. in 2014). Researchers reported the presence of 943,395 genes unique to the Indian gut microbiome, which were not previously listed in the IGC and this led them to create an updated gene catalogue by adding 9% novel genes. The study’s lead contact, Dr. Sharma, says that the upgraded gene set, with India-specific genes appended, will serve as a more comprehensive reference for global gut microbiome studies in the future.

Prevotella emerged as the most dominant genus and the key bacterial marker of the Indian gut microbiome. The gut microbiome of the cohort from north-central India, which primarily consumed a plant-based diet, was found to be associated with bacterial species of Prevotella, and also showed an enrichment of Branched Chain Amino Acid (BCAA) and lipopolysaccharide (LPS) biosynthesis pathways. Along with Prevotella, the other genera that co-occurred were Mitsuokella, Lactobacillus and Megasphaera. In contrast, the gut microbiome of the cohort from southern India, which consumed an omnivorous diet, showed associations with bacterial species of Bacteroides, Ruminococcus and Faecalibacterium, and had an enrichment of Short Chain Fatty Acid (SCFA) biosynthesis pathway and BCAA transporters.

The largest fecal metabolome study from India: Metabolomics of fecal and serum samples was also performed and correlated with gut microbiome for the first time on such a large dataset in India. The results 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.

The study provides the first functional insights into the unique and under-explored Indian gut microbiome. The functional associations revealed using metagenomic and metabolomic approaches underscore the significance of the gut-microbe-metabolic axis in human health, which will find enormous applications when devising region- and diet-specific probiotics and prebiotics, and are also much needed for future epidemiological and translational research.



Dhakan DB, Maji A, Sharma AK, et al. The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches. GigaScience. 2019; 8(3):1-20. doi: 10.1093/gigascience/giz004.

Pulikkan J, Maji A, Dhakan DB, et al. Gut microbial dysbiosis in Indian children with autism spectrum disorders. Microb Ecol. 2018; 76(4):1102-14. doi: 10.1007/s00248-018-1176-2.

Maji A, Misra R, Dhakan DB, et al. Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers. Environ Microbiol. 2018; 20(1):402-19. doi: 10.1111/1462-2920.14015.

Saxena R, Mittal P, Clavaud C, et al. Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. Front Cell Infect Microbiol. 2018; 8:346. doi: 10.3389/fcimb.2018.00346.

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Li J, Jia H, Cai X, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014; 32:834-41. doi: 10.1038/nbt.2942.

Vineet K. Sharma
Vineet K. Sharma
Dr. Sharma has been an Associate Professor at the Indian Institute of Science Education and Research Bhopal since July 2011. Dr. Sharma obtained his PhD in Bioinformatics and Biomedical Sciences from IGIB, New Delhi in 2006. After completing his doctoral research, he worked as a scientist at RIKEN, Japan for five years and joined IISER Bhopal after returning to India. He is also the founder and coordinator of the Innovation and Incubation Centre of Entrepreneurship (IICE) at IISER Bhopal. The main focus of Dr. Sharma’s lab is to reveal and analyze the human-associated microbiome among the Indian population and carry out comparative studies with different populations to gain functional insights, while also making comparisons with healthy and disease datasets. Dr. Sharma’s groups also recently sequenced the genome of the peacock, which is the national bird of India.