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. 2021 Jul 5;6(8):1043–1054. doi: 10.1038/s41564-021-00920-0

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 1 — Fifteen men and women provided stool samples, and underwent a session of colonoscopy, during which luminal aspirates were collected from the terminal ileum, cecum, and descending colon; and mucosal brushes were collected from the cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. As a validation to the analysis in Fig. 1, metagenomic sequences were subsampled to 1.5 M reads, resulting in 66 stool (blue), 29 lower GI luminal aspirates (light green), 14 terminal ileum luminal aspirates (peach), and 39 lower GI mucosal brush (dark green) samples analyzed using ShortBRED & CARD for identifying and quantifying ARGs. a, Bray-Curtis dissimilarity of stool and endoscopic samples, based on ARG families. PC1 stool vs. TI lumen P = 0.002,, stool vs. lower GI mucosa P = 0.025, stool vs. lower GI lumen P < 0.0001; PC2 stool vs. lower GI mucosa P = 0.0175. b, Bray-Curtis dissimilarity to stool in samples from the TI lumen (P = 0.0139), lower GI mucosa (P = 0.0187), and lower GI lumen (P = 0.0027), based on ARG families. c, Observed ARGs ‘subtypes’ (ARG-OAP v2.0, alpha diversity) is lower in stool compared to the lower GI mucosa (P = 0.0012) and lower GI lumen (P = 0.0008). d, Observed ARGs using CARD & ShortBRED is lower in stool compared to TI lumen (P = 0.0213), lower GI mucosa (P = 0.0027), lower GI lumen (P = 0.0016). e, Abundance of drug classes per region. f, Drug classes significantly overrepresented in the GI (red) or stool (blue). Colored circles represent P < 0.05 (FDR-corrected two-sided Mann-Whitney). g, Observed genera (alpha diversity), rarefied to 2 M reads, is higher in stool compared to TI lumen (P < 0.0001), lower GI mucosa (P = 0.0015), and lower GI lumen (P < 0.0001). h, Spearman correlation (P < 0.0001) of Escherichia abundance with observed drug class. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001, Kruskal-Wallis & Dunn’s. Horizontal lines represent the median, whiskers 10-90 percentiles. GI, gastrointestinal tract; TI, terminal ileum.

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