Figure 5: Microbiota composition differs between immune-competent and immune-compromised hosts.

(a) Microbiota composition at the genus level of 10 WT and 10 Rag2^−/− mice from the day 3 of the evolution experiment (streptomycin-treated and colonized with E. coli). Genera with a relative abundance larger than 1% are displayed. The coloured segments represent the relative frequency of each genus. (b) Relative frequencies of genera differentially represented in WT and Rag2^−/− animals: Barnesiella (Mann–Whitney U-test with the Benjamini and Hochberg correction, W=11, P=0.021), Bacteroides (Mann–Whitney U-test with the Benjamini and Hochberg correction, W=18, P=0.049), Paenibacillus (Mann–Whitney U-test with the Benjamini and Hochberg correction, W=14.5, P=0.029), unclassified Clostridiales (Mann–Whitney U-test with the Benjamini and Hochberg correction, W=6, P=0.0065) and Allobaculum (Mann–Whitney U-test with the Benjamini and Hochberg correction, W=13, P=0.025). *P<0.05, **P<0.01. Alpha diversity estimates of microbiota community richness (c), diversity (d) and phylogenetic diversity (e) in WT and Rag2^−/− animals. Both OTU-based diversity and phylogenetic diversity are increased in Rag2^−/− animals compared with WT (Mann–Whitney U-test, W=20, P=0.03 and W=17, P=0.01, respectively). NS, not significant; P>0.05, *P<0.05. Principal coordinate analysis (PCoA) of the Bray–Curtis (f) and weighted UniFrac (g) distance matrices of faecal microbiota of WT and Rag2^−/− mice. The first two coordinates are shown. Ellipses centred on the averages of the metric distances with a 90% confidence interval for the first two coordinates were drawn on the associated PCoA.