Additional file 6 of Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications

Additional file 6 : Fig. 6. Enterotyping. Microbiota data from T-7 to T68 were aggregated at genus-level, filtered for “unknown” and “uncultured” attributions, and analyzed using the clustering approach described in [6] (“enterotyping”). Panel a, clustering score (Calinski-Harabasz index [36]) as a function of the number of clusters shows a maximum at 3 clusters. Panel b, clustering with 3 clusters. Panel c, correspondence between clusters in panel b and PCoA1-based microbiota states from Fig. 2 (1, basal state; 2, alternative state). Numbers indicate number of samples (Table 1) in each category. Microbiota state 2 roughly corresponds to cluster A. Panel d, Akkermansia, Phascolarctobacterium and Bacteroides distributions in clusters A, B and C. Combined data from T-7 to T68; each dot represents one intestinal microbiota sample. Abundance is expressed as number of sequence reads on a total of 38,000. Only genera for which the median abundances in the two microbiota states differ at least 1.2-fold with q < 0.05 (Wilcoxon test with FDR adjustment) are presented. The table presents q-values for pairwise comparisons of relative abundances between clusters, for each of the three species (Kruskal-Wallis test with posthoc Dunn’s test and Holm correction for multiple comparisons).