Figure 3

Differences between ileal and cecal microbiota of broiler chickens. Rarefaction curves for ileal and cecal bacteria, for the observed OTUs (A) and phylogenetic diversity (B) indices. Significant differences were seen between the alpha diversity indices of ileal samples and samples taken from cecum (nonparametric t-test, P < 0.01). PCoA analysis of OTUs (C) indicates that the bacterial profile differed strongly according to sampling site (R = 094, P = 0.001). Taxa significantly associated with ileal communities (green) versus cecal communities (red), shown in circular cladogram based on the Ribosomal Database Project (RDP) bacterial taxonomy (D). The cutoff value of linear discriminant analysis (LDA) was 2.0 or higher. Biomarker taxa are heighted by colored circles and shaded areas. Each circle’s diameter is relative to abundance of taxa in community.