Extended Data Fig. 2: HC and TB show significantly different diversity, composition and abundance of gut bacteria, and abundance of A. muciniphila and B. vulgatus are significantly higher in HC than TB at Foshan cohort.
(a) PCoAplot (based on Weighted UniFrac distances (HC = 17, TB = 19, Foshan cohort). (b) The relative abundance of gut bacteria in phylum level in the fecal samples from HC (n = 17) and TB (n = 19). (c) A. muciniphila was belonged to top 10 bacterial species in fecal microbiota of HC. Species with enriched relative abundance in HC are adjusted P < 0.05 and log2 (HC/TB) > 0, species with enriched relative abundance in TB are adjusted P < 0.05 and log2 (HC/TB) < 0. The red-boxed area marks the A. muciniphila. (d) The absolute abundance of A. muciniphila in the fecal microbiota from HC (n = 17) and TB (n = 19). (e)Predictive power of top 10 species enriched in HC (that is the top 10 most reduced species in TB) assessed by random forest analysis. Blue boxplots correspond to minimal, average, and maximum Z-score of shadow species, which were shuffled version of real species introduced to random forest classifier and act as benchmarks to detect truly predictive species. Red boxplots represent rejected species, yellow boxplots represent suggestive species, and green boxplots represent confirmed species. The red arrowhead marks the A. muciniphila. HC = 17, TB = 19. (f) Histogram of the Linear discriminant analysis (LDA) coupled with effect size measurements (LEfSe) identified the species with different abundance in HC and TB. Higher abundant species in TB are shaded in green, higher abundant species in HC are shaded in red. Red arrowhead pointed A. muciniphila, black arrowhead pointed B. vulgatus. (g) Circle charts showed the relative abundance of six bacteria with differentiated relative abundance between HC and TB in Foshan cohort, and these six bacteria were also observed at both Shenzhen and Foshan cohorts. Histogram showed the fold change of relative abundance of six bacteria, including B. vulgatus, B. uniformis, A. muciniphila, B. caccae, P. merdae and E. ramosun between HC and TB (calculated as HC/TB) in Foshan cohort. Bacteria are identified by color bars above the chart. Data are presented as mean + /- SD. Pvalue was calculated by PERMANOVA test (a), Mann-Whitney test [(c)and (d)].
