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. 2022 Apr 1;8:15. doi: 10.1038/s41522-022-00276-1

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© The Author(s) 2022

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. 1 — a C. difficile challenge experimental design. The figure legend at the left panel indicates the samples sizes for 2 cohorts; more information on batching and n’s per assay is given in Supplementary Table 2. Cohort 1 was followed for 13 days post C. difficile gavage to monitor survival and gut microbiome composition over time. Cohort 2 was sacrificed at 3 days post C. difficile gavage to collect cecal contents for measurement of metabolites and toxin and colon and cecal mucosa for histopathology (some assays were only conducted on a subset of Cohort 2, but all in at least two independent experiments; see Supplementary Table 2 for details). Gray and orange boxes indicate the time points at which samples were collected for the respective cohorts. b Survival curves on the three diets. Statistical significance as assessed by log-rank comparison is indicated.