Fig. 2

Host genetic-specific associated with the compositions and functions of wild giant panda gut microbiomes. A Alpha diversity of gut microbiomes among the three wild genetic populations (n = 45). The FDR-corrected Wilcoxon rank sum test was used to determine significance. **p < 0.01, *p < 0.05. The following group colors are the same as in A. B Principal coordinates analysis revealed two distinct clusters of microbial communities along the first principal component belonging to the QIN and QXL populations, respectively, with MIN communities exhibiting mixed compositions. The solid and empty ellipses were constructed based on multivariate normal distributions at 50% and 70% confidence levels, respectively. C Bar plot showing the assemblage patterns of giant panda gut microbiota at the genus level. Patterns were determined based on hierarchical clustering. D Characterization of host genetic-specific genes and KEGG pathways of gut microbiomes. Venn diagrams showing shared and unique genes in the gut microbiomes of each genetic population. The bar plot shows the gene counts at the second KEGG pathway level for each pairwise comparison. The inset bar graph shows the total numbers of microbial genes in each population annotated to KEGG orthologs. E Hierarchy of KEGG pathways showing the functional differentiation of gut microbiomes among the three genetic populations based on LEfSe analysis. Pathways with LDA > 2 and p < 0.05 are shown. The numbers refer to pathways designated in Fig. S8A