Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh

Abstract

Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.

Fig. 1. The abundance of the top prevailing bacterial genera, archaeal features, core features, and Firmicutes to Bacteroidetes ratio in various Bangladeshi cohorts.

a The bar plot represents the normalized frequency of the top genera among different cohorts (b) Several archaeal species appeared to be present in different samples from each cohort. c The frequency of core features resulted in two primary clusters, with somewhat varied abundances in some Bengali samples. d The median ratio of Firmicutes to Bacteroidetes.

Fig. 2. Distribution of alpha diversity in terms of Shannon diversity and observed features among various Bangladeshi ethnic cohorts.

The Kruskal–Wallis test for all groups had a p-value of 0.0033. Chakma, Marma, Khyang and Tripura populations had higher species richness than the Bengalis (p-value = 0.0003) (n = 54 biologically independent samples).

Fig. 3. Distribution of alpha diversity in terms of Faith phylogenetic diversity and Pielou evenness among various Bangladeshi ethnic cohorts.

The difference in Faith pd score was statistically insignificant (p-value = 0.3816). There was no significant difference in Pielou evenness profile between indigenous populations (p-value = 0.0631) (n = 54 biologically independent samples).

Fig. 4. Beta diversity clustering between various Bangladeshi ethnic cohorts.

The diversity was measured using (a) Bray–Curtis matrix (b) Jaccard distance matrix (c) Unweighted unifrac distance (d) Unweighted unifrac distance.

Fig. 5. Differential abundance of gut microbes of various ethnic groups in Bangladesh.

a ANCOM analysis of Bengali people (b) ANCOM analysis of Chakma people (c) LEfSe analysis of Bengali, Chakma, Marma, Khyang, and Tripura people (n = 54 biologically independent samples).

Fig. 6. Functional analysis of enriched pathways in Bengali, Chakma, and Marma population.

a Bengali (b) Chakma, and (c) Marma groups showed differential enrichment of function.

Fig. 7. Comparative diversity analysis between Bangladesh and several other tropical and subtropical countries.

a Bray–Curtis matrix (Red circle encircles Bangladeshi samples) (b) Jaccard distance matrix (Red circle encircles Bangladeshi samples) (c) Unweighted unifrac distance (d) Unweighted unifrac distance (e) Faith phylogenetic diversity (p-value = 2.3238) (f) Observed features (p-value = 1.6253) (g) Pielou evenness (p-value = 9.3489) (h) Shannon diversity (p-value = 6.0806) (n = 55 biologically independent samples).

Fig. 8. Unweighted pair group method with arithmetic mean based gut microbiome clustering of Bangladeshi and several other tropical and subtropical countries.

Majority of the Bangladeshi indigenous samples clustered with Indian indigenous groups.