Figure 6. Gut microbiome following adolescent cafeteria diet consumption.

(A and B) PCoA plots of CAF-exposed rats gut microbiomes when analyzed either in Experiment 1A (no healthy dietary intervention) or in Experiment 1B (after healthy dietary intervention). Ellipses indicate 95% confidence limits. R² and P are from PERMANOVA tests. (C) Shannon index of CAF-exposed rats gut microbiomes either before or after healthy dietary intervention. The differences were tested with Wilcoxon tests. (D and E) Significant differential taxa between treatment and chow-fed rats at phylum to species level (Wilcoxon test, FDR<0.1) are highlighted on the phylogenetic trees of all taxa identified in this study. An FDR cutoff of 0.1 was used here for visualization. (F) The correlation plots of Deferribacteraceae in Experiment 1A, Proteobacteria, Actinobacteria (phylum), Cyanobacteria and Ruminiclostridium in Experiment 1B with NOIC performance (% shift from baseline discrimination index on test day) across CAF and CHOW samples. Spearman’s correlation was used for the analysis and P-values were corrected for multiple hypotheses testing with the Benjamini-Hochberg method. CHOW: chow-fed; CAF: cafeteria diet; PCoA: Principal Coordinate Analysis; FDR: false discovery rate; rho: Spearman’s ρ