Panel A shows a box plot representing the mean alpha diversity of fecal microbiota (Shannon index) at different time points (Day 0, Day 29, Day 84/85) for both sham and Bb-infected groups. The y-axis represents the Shannon index, and the x-axis represents the different groups and time points. Panel B is a scatter plot showing Principal Coordinate Analysis (PCoA) of beta diversity, with the x-axis labeled PCoA 1 (33.3 percent) and the y-axis labeled PCoA 2 (29.3 percent). Different colors represent different groups and time points. Panel C consists of multiple heat maps representing the mean read counts of operational taxonomic units (OTUs) that showed significant changes in either or both Day 29 and Day 84/85 Bb mice compared to sham-infected controls. The heat maps are categorized by different bacterial groups such as Bacteroidota, Firmicutes, Actinobacteria, Verrucomicrobiota, and others. The color scale indicates the read counts. Panel D shows box plots representing the mean concentrations of different short-chain fatty acids (acetic acid, butyric acid, propionic acid, valeric acid, hexanoic acid) at different time points (Day 0, Day 29, Day 84/85) for both sham and Bb-infected groups. The y-axis represents the concentration in mmol/kg, and the x-axis represents the different groups and time points. Each symbol represents data from one mouse. The graphs collectively illustrate the changes in microbial diversity and short-chain fatty acid concentrations over time in Bb-infected and sham-infected mice.
Changes to the GI microbiome of Bb-infected mice. Fecal samples were collected from Bb-infected and control sham-infected mice (n = 12/group) at 0, 29, and 84/85 dpi for 16S rRNA sequencing and SCFA analyses. (A) Mean ± SEM α diversity of fecal microbiota (Shannon index). (B) PCoA of β diversity, assessed by calculating Bray–Curtis dissimilarities from OTU abundance. (C) Heat map representing the mean read counts of OTUs (Data S1) that showed significant changes in either or both day 29 and day 84/85 Bb mice compared with sham-infected controls. (D) Mean ± SEM concentrations of indicated SCFAs. Each symbol represents data from one mouse. (A–D) Each time point represents part of a longitudinal study following the same group of mice over time. One-way ANOVA, *P < 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001, and ns, not significant (P > 0.05). PCoA, principal coordinate analysis.