Metagenomics analysis reveals features unique to Indian distal gut microbiota

Abstract

Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrateactive enzymes in the gut microbiota as compared to the other countries. OPEN ACCESS Citation: Kaur K, Khatri I, Akhtar A, Subramanian S, Ramya TNC (2020) Metagenomics analysis reveals features unique to Indian distal gut microbiota. PLoS ONE 15(4): e0231197. https://doi.org/ 10."Man as a superorganism: Understanding the Human Microbiome (HUM-CSIR-BSC0119)". Funder URL: https://www. csir.res.in/ The funders had no role in study design, immunomodulation [13], defense against pathogens [14], nutrient and energy harvest, and metabolism [15][16][17][18]. Considering the important role of the gut microbiome in maintaining homeostasis, it is important to understand the microbial diversity and the functional metagenome of the healthy gut.Despite the fact that significant intra-and inter-individual variations exist in the taxonomic composition of microbial communities in the human distal gut, there are several initiatives aiming to find common patterns among two or more different groups of interest. Identifying the differences and similarities among the healthy gut microbiota between two geographies has been important to understand the impact of the environment and diet. With this aim, several metagenomics initiatives have been taken in several regions across the world such as China [7,18], Russia [19], Europe [20,21], USA [22], Venezuela [1], Africa [23], Ireland [2], Italy [24], Japan [25] and Korea [26]. Several studies have previously been performed on Indian subjects, too, with their wide focus on healthy and malnourished children [27,28], le...

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“…Contrary in India, Prevotella copri and Faecalibacterium prausnitzii (Pulipati et al, 2020) from the butyrate producing bacteria lineages (Kaur et al, 2020), are the most predominant core bacterial genera as identified in the 'Landscape of Gut Microbiome-Pan India Exploration' (LogMPIE) study results suggesting that the majority of Indian populations are still adhering to the whole grains, legumes and plant-based diet (Kaur et al, 2020). However, this result was not in agreement with the smaller cohort study conducted in unique geographical locations (Das et al, 2018).…”