Fig. 5
Microbiota promotes macrophage inflammatory response. A Principal component (PCA) analysis of macrophage transcriptomic profiles compared at 7 days pi between cells from conventional (blue), GF (red) and GF chickens receiving a microbiota from conventional chickens at 4 days pi (green). PERMANOVA statistical test result is showed on the upper right corner and in the table. *P < 0.05. Each point on PCA plots represents an animal and a larger dot corresponds to the barycenter according to each group. Dim1 axis and Dim2 axis show principal components 1 and 2 and the percent variation corresponding to each component are shown in parenthesis. Differential gene expression was determined for infected conventional versus (vs) infected GF (B), infected GF + microbiota vs infected GF (C) and infected GF + microbiota vs infected conventional (D), infected GF + microbiota) and are represented as volcano plots. Scattered dots represent each gene. Only significantly different gene expression (P < 0.05) and fold change > 2 or < -2 are indicated. These thresholds are indicated with dashed lines on the plots