Fig. 3

Seasonal gut microbiome variations and associations between the fecal metabolome and metagenome. Comparison between shotgun sequencing data of stool samples from the leaf season (WL, n = 28; CL, n = 27) and shoot season (WS, n = 24; CS, n = 21). A Rarefaction curves based on gene count. B Box plot of the gene count in four groups. C β-Diversity (Bray-Curtis similarity index) of the four groups at the gene level. D Box plot of the number of metagenomic species (MGS) in the four groups. For B, C and D, a two-tailed Wilcoxon rank-sum test was used to determine significance. *P value < 0.05, ***P value < 0.001. NS, not significant. Boxes represent the interquartile ranges (IQRs) between the first and third quartiles, and the line inside the box represents the median; whiskers represent the lowest or highest values within 1.5 times the IQR from the first or third quartiles. Circles represent data points beyond the whiskers. A plot of the first two axes (Axis1 and Axis2) of a CoIA of fecal metabolites and all CAGs of captive (E) and wild samples (F). Covariation showed concordance of seasonal structural shifts between fecal metabolites and all CAGs. Each sample is represented with an arrow. Green and magenta colors represent the leaf eating season and shoot eating season, respectively. The sample projections in the metabolome and metagenome space are represented by the starting point and the end of the arrow, respectively. The length of the arrow is inversely proportionally to the consensus between these two datasets. G Correlation network between fecal metabolites (five monomers representing five subclasses of flavonoids) and the metagenomic species (MGS) that were different between seasons. For clarity, only significant strong correlations (Spearman’s rank correlation: |r| > 0.6, P < 0.05) were considered. Red and blue edges denote Spearman’s rank correlation coefficient r > 0.6 and r < -0.6, respectively. The numbers in parentheses next to each species name represent the number of genes in the MGS