Fig. 6

Associations between bacterial genera and intestinal gene expression, short-chain fatty acids and alpha-diversity. a Heatmap of Spearman’s rank correlation coefficients between the relative abundance of genera (with a minimum prevalence of 50% across all samples) at 4 weeks of age (P4W) and levels of SCFAs, gene expression and bacterial diversity. The colour bar shows the taxonomic classification of included genera at phylum level (blue: Firmicutes, red: Bacteroidetes, green: Proteobacteria, yellow: Actinobacteria and pink: Tenericutes). b Heatmap of Spearman’s rank correlation coefficients between concentrations of specific bile acids in serum and colon and gene expression in colon of bile acid receptors FXR and TGR5. Colour bars indicate primary (green), secondary (orange), conjugated (black) and unconjugated (grey) bile acids. In both panels, *p < 0.05; **p < 0.01 and ***p < 0.001