Fig. 1: ARG characteristics of different bacteria in the adult gut and bimodal distribution of ARGs in the adult gut, driven by E. coli. | Nature Communications

Fig. 1: ARG characteristics of different bacteria in the adult gut and bimodal distribution of ARGs in the adult gut, driven by E. coli.

From: Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

Fig. 1

a The total abundance of ARGs resistant to 33 drug classes. b Total ARG abundance in the bacterial species (left), mean relative abundance of ARGs in bacterial species (middle), and ARG richness in bacterial species (right). For ease of viewing, only the 63 species with the highest ARG abundance are listed. c Heatmap depicting the abundance of 293 ARGs across the samples. Samples and ARGs were individually clustered with complete linkage hierarchical clustering and PAM clustering based on Euclidean distance. Cluster 4 (core ARGs, N = 15) contained highly abundant and prevalent ARGs across all samples. Cluster 3 (differentially abundant (DA) ARGs, N = 55) contained ARGs with significant abundance differences among samples. Cluster 2 (low-abundance (LA) ARGs, N = 80) contained ARGs present at a low abundance. Cluster 1 (intermediate-abundance (IA) ARGs, N = 143) contained ARGs with intermediate abundance, falling between those in cluster 4 and cluster 2. d Density plot of ARG richness in the cohort. e Average silhouette width of PAM clustering for k = 1 to 10 clusters. f, g Log-transformed total ARG abundance and observed ARG richness (α-diversity) (f), and NMDS ordination plot of Bray–Curtis dissimilarity matrix of ARG abundances (g) before (left) and after (right) the removal of E. coli ARGs from the two ARG PAM clusters (Ncluster 1 = 87, Ncluster 2 = 130). The box plot displays 25th, 50th (median), and 75th percentiles, with whiskers extending 1.5 * IQR. The percent of explained variance (R2) generated with the PERMANOVA test is shown in the figure. h Relative abundances of 16 species (of 542 in total) that differed in abundance between the two clusters. Relative abundance on the x-axis is shown on a logarithmic scale; black dots indicate median value; P-values were generated by the Wilcoxon rank-sum test, and FDR adjustments are represented as adjusted P-values. All P-values were derived from two-sided tests.

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