Fig. 2

Comparison of gut microbiome in different intestinal compartments of chickens. a Microbial diversity (Shannon index) at gene, genus, OG, and KO levels. Box plots show median ± interquartile range (IQR) and 1.5 IQR ranges (whiskers), with outliers denoted by dots. b The non-metric multidimensional scaling (NMDS) plot based on Bray-Curtis dissimilarities at species level. An obvious difference was observed between the foregut (duodenum, jejunum, and ileum) and hindgut (cecum and colorectum). c Differences in microbial functions between the foregut and hindgut based on KEGG functional categories (Wilcoxon rank-sum test, Storey’s methods for multiple tests adjustment). Chicken gut microbial co-occurrence network analysis based on core genus (average relative abundance > 0.1%) d in the foregut and e hindgut. Solid line: Spearman’s rank correlation coefficient > 0.30; dash line: Spearman’s rank correlation coefficient < − 0.30. The size of nodes was proportional to the relative abundance of genera