Fig. 2

Taxon-independent multivariate analysis and separation of broiler microbiota. a Discriminant analysis of principal components revealed distinct clustering of the control (NC, grey), Salmonella-challenged (SC, white), and Bacillus-treated (BT, black) groups using OTU at the 97% identity level. Significant differences (P < 0.001) were calculated using compare_categories.py using the PERMANOVA test. b Canonical loading plot showing differentially abundant bacterial genera. The individual peaks show the magnitude of the influence of each variable on separation of the NC, SC, and BT groups after challenge of broiler chickens (0.05 threshold level)