Gut Microbial Profile Is Associated With Residential Settings and Not Nutritional Status in Adults in Karnataka, India

Abstract

Undernutrition is a leading contributor to disease and disability in people of all ages. Several studies have reported significant association between nutritional status and gut microbiome composition but other factors such as demographic settings may also influence the adult microbiome. The relationship between undernourishment and gut microbiome in adults has not been described to date. In this study, we compared the gut microbiome in fecal samples of 48 individuals, from two demographic settings (rural and urban slum) in Karnataka, India using 16S rRNA sequencing. Nutritional status was assessed based on BMI, with a BMI of < 18.5 kg/m² classified as undernourished, and a BMI in the range 18.5-25 kg/m² as nourished. We analyzed 25 individuals from rural settings (12 undernourished and 13 nourished) and 23 individuals from urban slum settings (11 undernourished and 12 nourished). We found no significant difference in overall gut microbial diversity (Shannon and Unweighted UniFrac) between undernourished and nourished individuals in either geographical settings, however, microbial taxa at the phylum level (i.e., Firmicutes and Proteobacteria) and beta diversity (unweighted UniFrac) differed significantly between the rural and urban slum settings. By predicting microbial function from 16S data profiling we found significant differences in metabolic pathways present in the gut microbiota from people residing in different settings; specifically, those related to carbohydrate and lipid metabolism. The weighted sum of the KEGG Orthologs associated with carbohydrate metabolism (Spearman's correlation coefficient, ρ = -0.707, p < 0.001), lipid metabolism (Spearman's correlation coefficient, ρ = -0.330, p < 0.022) and biosynthesis of secondary metabolites (Spearman's correlation coefficient, ρ = -0.507, p < 0.001) were decreased in the urban slum group compared to the rural group. In conclusion, we report that the geographical location of residence is associated with differences in gut microbiome composition in adults. We found no significant differences in microbiome composition between nourished and undernourished adults from urban slum or rural settings in India.

Keywords: BMI; adults'; gut microbiota; rural—urban linkages; undernourished.

Figure 1

Box and Whisker plot depicting relative abundance of significant phylum. (A) Firmicutes and (B) Proteobacteria in undernourished and nourished from rural and urban-slum settings. p-values indicate statistical significance from independent t-tests comparing nourished and undernourished study groups in both the locations (i.e., rural normal vs. rural undernourished and urban normal vs. urban-undernourished) and independent t-test based on location (i.e., rural vs. urban-slum). Box-and-whisker plots show high, low, and median values, with lower and upper edges of each box denoting first and third quartiles, respectively. ns indicates non-significant p-values. Black dots represent the outliers.

Figure 2

Box and Whisker plot depicting. (A) Shannon Diversity (α diversity index) in undernourished and nourished from urban and rural settings; (B) Beta Diversity (unweighted Unifrac distances) in undernourished and nourished in urban and rural settings. p-values indicate statistical significance from independent t-tests comparing nourished and undernourished study groups in both the locations (i.e., rural normal vs. rural undernourished and urban normal vs. urban-undernourished) and independent t-test based on location (i.e., rural vs. urban-slum). Box-and-whisker plots show high, low, and median values, with lower and upper edges of each box denoting first and third quartiles, respectively. ns indicates non-significant p-values. Black dots represent the outliers.

Figure 3

Principal Coordinates Analysis (PCoA) of the similarity across the study groups based on the nutritional status (nourished vs. undernourished) and location (rural vs. urban slum) based on the Unweighted UniFrac distances. Each point corresponds to a sample colored according to the nutritional status and corresponding location and the size of the point corresponds to the Shannon diversity index. Principal Coordinates (PC) axis expresses the percent variance across the samples.

Figure 4

Box and Whisker plot depicting the relative abundance of significant taxa associated with undernourished and nourished from urban slum and rural settings. p-values indicate statistical significance from independent t-tests comparing nourished and undernourished study groups in both the locations (i.e., rural normal vs. rural undernourished and urban normal vs. urban-undernourished) and independent t-test based on location (i.e., rural vs. urban-slum). Box-and-whisker plots show high, low, and median values, with lower and upper edges of each box denoting first and third quartiles, respectively. ns indicates non-significant p-values. Black dots represent the outliers.

Figure 5

Box and Whisker plot depicting the pathways significantly associated with undernourished and nourished from urban slum and rural settings in (A) Carbohydrate metabolism (p < 0.001), (B) Lipid metabolism (p = 0.006), (C) Biosynthesis of secondary metabolites (p < 0.001). p-values indicate statistical significance from independent t-tests comparing nourished and undernourished study groups in both the locations (i.e., rural normal vs. rural undernourished and urban normal vs. urban-undernourished) and independent t-test based on location (i.e., rural vs. urban-slum). Box-and-whisker plots show high, low, and median values, with lower and upper edges of each box denoting first and third quartiles, respectively. ns indicates non-significant p-values. Black dots represent the outliers.