Fig. 4

Colonization by the E. coli consortia alters the structure of the stool and mucosal microbiome of the inflamed colon. A, B PCoA based on Bray–Curtis distance for the stool (A) and mucosal (B) microbiome in Il10^−/− mice that received FMT1 with (red) or without (blue) E. coli. C, D PCoA based on Bray–Curtis distance for the stool (C) and mucosal (D) microbiome in Il10^−/− mice that received FMT2 with (red) or without (blue) E. coli. E, F The Shannon diversity index for the stool (E) and mucosal (F) microbiome in Il10^−/− mice that received FMT1 with (red) or without (blue) E. coli. Each symbol represents an individual mouse, n = 9–17 mice per group. Circles in A–D represent 95% confidence limits. Box and whisker plots show the median, first/third quartiles, and min/max index values. G Relative abundance (% of total barcoded reads) of 7 barcoded E. coli strains colonizing the distal colon mucosa and stool of Il10^−/− mice that received FMT1 or FMT2. Bars associated with Il10^−/− cohort “7E.coli + FMT1” are also included in Fig. 3A for another comparison. H Microbiome composition of the distal colon mucosa and stool in Il10^−/− mice that received FMT1 or FMT2 without E. coli. Rare genera with < 1% abundance in any of the samples were collapsed together. Unassigned sequences that could not be classified with accuracy at the phylum level were removed; g—genus, f—family