Fig. 2

Lack of soluble fiber, not fat, significantly alters gut microbiota composition in young adult and 1-year aged female mice. a Principal coordinates analysis comparing fecal microbiota community structure between females consuming chow and refined diet, demonstrating the significant effect of chow and refined diet on community structure (PERMANOVA, F = 26.284, r² = 0.614, P < 0.0001), accounting for 67.4% of variance. No difference in community structure between rLFD and rHFD females was observed (PERMANOVA, F = 1.75, r² = 0.074, P = 0.132). b Additional principal coordinates analysis comparing fecal microbiota community structure between young adult and aged females consuming chow, rLFD, and rHFD, demonstrating significant interactions of age, rLFD, and rHFD on community structure (PERMANOVA, F = 10.122, r² = 0.614, P < 0.001). c, d Comparison of community diversity in young adult and aged females consuming chow, rLFD, and rHFD. c The alpha diversity measure, observed species, plotted against sampling time point demonstrating no impact of diet transition and consumption of refined diets on the number of unique taxa (Kruskal-Wallis, H = 9.45, P = 0.22). d The alpha diversity measure, Shannon diversity index, plotted against sampling time point shows significant differences in community richness and evenness in young adult and aged females (Kruskal-Wallis, H = 26.647, P = 0.00038). e Stacked barplot showing the average relative abundance of taxa in chow, rLFD, and rHFD young adult and aged females, characterized by a rapid and lasting loss of taxa within the Bacteroidetes phylum and concomitant bloom of taxa within the Firmicutes and Proteobacteria phyla. Taxa key is truncated to display the 18 most abundant taxa. f Heatmap depicting 34 significantly different taxa by age and diet in females identified by linear discriminant analysis (FDR < 0.05). Columns represent taxa within each cage. N = 3 female cages/age/diet sampling time point. Data represented as individual data points average per cage ± SEM