High throughput sequence profiling of gut microbiome in Northern Indian infants during the first four months and its global comparison

The present study characterized the colonization and development of gut microbial communities in healthy Indian infants from North-Western Himalayan region in the province Himachal Pradesh. The diversity and transitions of core genera was assessed targeting the 16S rRNA V3-V4 hypervariable region on an Illumina platform. Analysis of more than 17,000 filtered high quality reads indicated that the diversity was lowest in the month 2 followed by gradual increase towards month 4 (1.24 folds increase in Shannon index). The microbial population in month 1 was dominated by Firmicutes and Proteobacteria followed by dominance of Actinobacteria and Firmicutes in the month 4. The analysis of aggregate microbiota at class level indicated relatively higher abundance of Clostridia, Bacteroides and Actinobacteria in month 1, 3 and 4, respectively. The global comparison of dominance of different phyla with the similar subjects indicated that the Indian microbiome is more similar with studies conducted with Swedish infants, although the differences in DNA extraction protocols, geographical location and sequencing platforms as confounding factors cannot be neglected. The findings in this small cohort study could facilitate future studies exploring various aspects of the human gut microbiome in Indian subcontinent.