Fig. 3 | Nature Communications

Fig. 3

From: Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line

Fig. 3

Alpha/beta diversities and most differentially abundant taxa of micro- and mycobiota for classes (diet and disease) in NZM2410/J mice. a Alpha diversity (Chao1 index, species richness) of microbial species between NZM2410/J mice set on three dietary regimens across the naive, transient, and final stages of disease development stratified based on caloric restriction (n = 18), control (n = 16) or western (n = 20) diet (left panel) or absence (n = 31) and presence (n = 23) of disease (right panel). b Alpha diversity (Shannon index, species richness) of the mycobiota between mice set on different diets across naïve, transient and final stages of disease stratified based on caloric restriction (n = 12), control (n = 12) and Western (n = 10) diets (left panel) or presence (n = 15) and absence (n = 19) of disease (right panel). c Principal coordinate analysis (PCoA) of beta diversity for the microbiota at the final stage of disease based on unweighted UniFrac distances between NZM210/J mice classified based on caloric restriction (n = 18), control (n = 16) or western (n = 20) diets (left panel) or presence (n = 23) or absence (n = 31) of disease (right panel). d PCoA of beta diversity for mycobiota at the final stage of disease based on Jaccard distances between NZM210/J mice classified based on caloric restriction (n = 12), control (n = 12) and western (n = 10) diets (left panel) or presence (n = 15) or absence (n = 19) of disease (right panel). Differentially abundant (e) mycobiota and (f) microbiota taxa identified by the LEfSe algorithm (default parameters) at transient stage in diseased vs. non-diseased mice. In panels (ab), data is presented as means ± SEM and statistical significance was assessed using Kruskal–Wallis test with Mann–Whitney U test as a post hoc test. The p-values were adjusted using the Benjamini-Hochberg correction procedure. *Padj < 0.05, **Padj < 0.01. Data in panels (cd) were analyzed using the adonis function in R (permutations = 999). Source data for (af) are provided in the Source Data file

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