Fig. 2.

Two microbiota states. a Principal Coordinates analysis (PCoA) of ecological divergence between microbiota samples (Jensen-Shannon Divergence), based on OTU data aggregated at genus level. Each dot represents one intestinal microbiota sample. The analysis includes the data from all experimental groups, for T-7 up to T68 (n = 562 samples; cf Table 1). The dashed red line corresponds to the separation between the two normal distributions in the inset (frequency distribution of PCoA1 using the same samples) and in c. b Subsets of the data in a, for three experimental groups at T-1 and T68, respectively. Colors represent treatment groups as indicated. c Bimodal distribution of microbiota status. PCoA1 coordinates from the ordination plot in a as a measure of microbiota status are divided in categories with a range of 0.01, and the frequency of occurrence of each category is plotted. Top left: combined data from all groups (0% up to 3% DSS) for T-7, T-1, T63, and T68 (n = 232 samples). Bimodal graph overlay (density) and coloration according to the results of finite Gaussian mixture modeling using Mclust 5.4 [18]. Blue and red represent basal state and alternative state microbiota, respectively. Other plots: data for groups (% DSS) and time-points as indicated at the left and at the top of the figure, respectively. Coloration according to the bimodal distribution in the top left plot. Scale of the vertical axis is adjusted for each plot individually. *, bimodal (mixed normal) distributions according to Mclust 5.4 [18] when analyzing per-plot data (maximal value of the Bayesian Information Criterion (BIC), corroborated by bootstrap sequential Likelihood Ratio Testing (LRT): a p = 0.001 (cf Additional Table 3); b p = 0.004; c p = 0.032; d p = 0.027; e p = 0.01; f p = 0.04; g p = 0.03)