Extended Data Fig. 5: Percent of reads mapping to CAZymes and antimicrobial resistance genes vary across the intestinal tract and are driven by distinct taxa.
From: Profiling the human intestinal environment under physiological conditions
a) The percent of reads that mapped to a database of CAZymes (Methods) was determined using metagenomic sequencing of each sample. b) Data from (a) separated by subject. c) In intestinal samples, the log2(read count) of eight ASVs was positively correlated (Spearman) with the percent of reads that mapped to the CAZyme database. Only ASVs with P < 0.001 are shown. P-values from left to right, top to bottom: 1.8 × 10−6, 7.2 × 10−4, 1.1 × 10−24, 3.7 × 10−4, 3.7 × 10−4, 2.6 × 10−5, 3.7 × 10−4, and 3.7 × 10−4. d) The log2(ASV read count summed over family members) of the Bacteroidaceae family was significantly correlated (Spearman; P = 6.4 × 10−7) with the percent of reads from stool samples that mapped to the CAZyme database. No other families had P < 0.01. e) The number of CAZymes identified in strains isolated from the intestinal tract of subject 1, organized by species. Each circle represents a single strain, and horizontal lines (mostly hidden by the circles) represent the median. f) The percent of reads that mapped to a database of AMR genes (CARD, Methods) was determined using metagenomics sequencing of each sample and was higher in devices compared with stool (P = 0.03). g) Data from (f) separated by subject. h) In intestinal samples, the log2(read count) of two ASVs was positively correlated (Spearman) with the percent of reads that mapped to CARD. Only ASVs with P < 0.001 are shown. P-values from left to right, top to bottom: 5.7 × 10−8, 1.5 × 10−4, 4.1 × 10−7, 2.5 × 10−4, 6.4 × 10−5, 2.0 × 10−8, and 2.1 × 10−4. i) In stool samples, the log2(ASV read count summed over family members) of families was significantly correlated (Spearman; P = 5.7×10−5, 1.5 × 10−3, and 7.1 × 10−4) with the percent of reads that mapped to a database of AMR genes. No other families had P < 0.001. j) The percent of reads that mapped to CARD ignoring all efflux pumps was similar between devices and stool (P = 0.8). k) log10(ratio of the number of AMR genes to bacterial genes) detected in each MAG, aggregated by family-level taxonomic assignment. Only MAGs with completion >75% and contamination <10% were included. In (a–d and f–j), each dot is a sample (n = 175 for devices and n = 58 for stool). All P-values reported are after Benjamini-Hochberg correction. Boxplots show the median and 1st and 3rd quartiles.
