Fig. 4

Characteristics of gut microbiome enterotypes and resistomes across wild and captive giant panda populations. A PCoA plot revealing three clusters in the gut microbiome, with each being significantly identifiable by variation in the relative abundances of Clostridium, Pseudomonas, and Escherichia. The lines connected to the center of each ellipse correspond to the affiliation. The inset mosaic plot shows the association between giant panda cohorts and enterotypes. The Pearson residuals were used to assess the individual contribution to the Pearson statistic. The blue, red, and grey colours correspond to positive, negative, and lack of associations, respectively. The area of each plot represents the sample size of each group. B The box plots show the relative abundances of major bacterial contributors of each enterotype. FDR-corrected Wilcoxon rank sum tests were used to determine statistical significance. ***p < 0.001, **p < 0.01, *p < 0.05. C Heatmap of antibiotic resistance genes (ARGs) identified among the three enterotypes. Information regarding resistance mechanisms and antibiotics is highlighted at the top. Color intensity indicates ARG abundances and darker colors indicate higher abundances. The sources and corresponding enterotypes of the sample in each line are marked in the tree (right)