Fig. 3

Gut microbiota is associated with host gene modules. A, B, C, and D Weighted gene co-expression network analyses (WGCNA) was performed to identify co-expressed gene modules (M). Gene modules are clusters of highly interconnected genes, which are designated by color codes (such as black M). The association of the two ecological groups with host gene modules was investigated by Pearson analysis. A and B represent association with gut and liver gene modules at week 1, and C and D represent association with gut and liver gene modules at week 3. Heatmaps show the correlation between gene modules and the two ecological groups of microbiomes. Clustering was performed by a complete clustering method using Euclidean distances. KEGG pathways enriched in the gene modules correlated with the functional groups (E and F). Enriched bubble plots have been shown for pathways with q-values < 0.05. Five or six biological replicates were included during analysis, $p < 0.1; *p < 0.05; **p < 0.01; ***p < 0.001