Fig. 1

C. difficile associated gut microbial community characteristics. (A) C. difficile colonization associated characteristics presented with non-metric multidimensional scaling (NMDS) plot illustrating beta diversity using Bray-Curtis dissimilarities, with colours indicating C. difficile colonization status and dot size representing C. difficile concentration. (B) Alpha diversity analysis depicted by Shannon diversity and Faith’s phylogenetic diversity. (C, D and E) C. difficile concentration (ddPCR; copies per ng DNA) associated changes in (C) mean Bray-Curtis dissimilarity, (D) Faith’s phylogenetic diversity and (E) Escherichia/Shigella (ZOTU1) relative abundance. All correlations are supported with Spearman’s rho and significance