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. 2021 Feb 2;12:755. doi: 10.1038/s41467-020-20793-x

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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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Fig. 2 — a Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from fecal pellets of Rag1^−/− and Rag1^HET mice prior to ABX treatment, at day 0 of infection, and at day 36 post-C. difficile infection or ABX-treatment alone. Ellipses signify different experimental groups. b Relative abundance of top 15 bacterial ASVs from C. difficile-infected of Rag1^−/− and Rag1^HET mice at day 36 p.i. Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. c Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity within and between C. difficile-infected Rag1^−/− and Rag1^HET groups at day 36 p.i. One-way ANOVA conducted for statistical comparison. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. d Dendrogram representation of intestinal microbial communities of C. difficile-infected of Rag1^−/− and Rag1^HET mice at day 36 p.i. using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. e mRNA expression of proinflammatory immune response genes in whole colon tissue as assessed by qRT-PCR. Gene expression relative to ABX-treated Rag1^HET mice and normalized to Hprt. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01. Data are presented as mean values ± SEM. f Proinflammatory cytokine and chemokine protein levels in cecal tissue homogenates. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Data are presented as mean values ± SEM. g Relative abundance of Proteobacteria and gamma-Proteobacteria ASVs in fecal pellets of Rag1^−/− and Rag1^HET mice at day 36 p.i. Statistical significance was calculated by a two-sided unpaired t test. Data are presented as mean values ± SEM. Data presented in figure are representative of three independent experiments. Prior to ABX treatment (n = 10 Rag1^−/−; n = 12 Rag1^HET mice), day 0 of infection (n = 6 Rag1^−/−; n = 5 Rag1^HET mice), day 36 post-C. difficile (n = 5 Rag1^−/− and Rag1^HET mice) or ABX-treatment alone (n = 2 Rag1^−/− and Rag1^HET mice).