Fig. 3
The core bacterial families identified within each of the GIT regions sampled in feedlot cattle. Each dot represents the relative abundance for a single sample for the core microbiota identified in luminal and intestinal surface samples by sampling location (rumen = RU, small intestine = SI, large intestine = LI, and feces), and by sample type (luminal content = LC, epithelial surface = ES). Core taxa were defined as bacterial families present in ≥ 90% of samples with ≥ 0.1% mean relative abundance. A total of 17 core families were identified in the rumen, 10 in the small intestine, 15 in the large intestine, and 20 in feces. Similar core community features were identified in luminal and epithelial surface samples from within tissues, and several families were shared across multiple locations, highlighting a gradient of microbial continuity throughout the GIT. Within-location comparisons revealed similar core community composition between luminal and mucosal samples, whereas across-location comparisons demonstrated both distinct core taxa by site, and prominent sharing of key features among locations that appear consistent with proximal-to-distal gradients in GIT function and structure.
