Fig. 1

Chicken gut microbial gene catalog. a Diagram of chicken intestinal tract. The microbial densities in the foregut and hindgut were labeled. b Rarefaction curves of detected genes from the whole set of 495 samples (Total) and from subgroups of LY, AA, and Distribution. A total of 9.04 million non-redundant genes were detected, and the rarefaction curve including all samples approaches saturation at the end of sampling. The gene number of a specific number of samples was calculated after random samplings repeated 100 times with replacement, and the median was plotted. c Venn diagram of gut microbial genes shared between the chicken, human, and pig catalogs. The criteria for shared genes were sequence identity > 95% and overlap > 90% of the shorter gene. d Taxonomic annotation of the chicken gut gene catalog at the superkingdom and phylum levels. e Venn diagram of KEGG orthologous groups (KOs) present in and shared by chicken, human, and pig catalogs. f Comparison of KEGG functional profiles (relative gene abundance summarized into KEGG functional categories and genes without functional annotations were excluded) of gut microbiome among chickens, humans, and pigs. Asterisks denote Wilcoxon rank-sum test result (P < 0.005)