Fig. 1: Diet modulates composition of intestinal fungi in the host.
From: Impact of diet and host genetics on the murine intestinal mycobiome
a Experimental design (created using Biorender). Mice were fed calorie restricted diet (CAL; nCAL = 250; nmales = 111; nfemales = 139), control diet (CON; nCON = 145; nmales = 54; nfemales = 91), or western diet (WES; nWES = 196; nmales = 63; nfemales = 133). We generated 427 ITS2 (nmales = 167; nfemales = 260), 557 16S rRNA DNA (nmales = 214; nfemales = 343), and 552 16S rRNA RNA (nmales = 215; nfemales = 337) samples from cecum. b Box plots representing the relative abundance of fungal phyla and genera. CAL (blue; nCAL = 188; nmales = 83; nfemales = 105), CON (gray; nCON = 108; nmales = 39; nfemales = 69), and WES (red; nWES = 131; nmales = 45; nfemales = 86) groups. The band in the box plot indicates the median, the box indicates the first and third QRs, and the whiskers indicate 1.5*IQR. (Ascomycota:PCAL-WES = 0.01; Basidiomycota: PCAL-WES = 0.01; Fungi_Un: PCAL-WES = 1.24 × 10−5, PCON-WES = 0.0009; Zygomycota: PCAL-WES = 0.04; Claviceps: PCAL-WES = 3.79 × 10−30, PCON-WES = 2.68 × 10−18; Davidiella: PCAL-WES = 1.35 × 10−11, PCON-WES = 6.59 × 10−7; Alternaria: PCAL-WES = 1.55 × 10−13, PCON-WES = 1.31 × 10−10; Wallemia: PCAL-WES = 0.001, PCON-WES = 0.0001). #Supplementary Data 2 shows statistical analysis of all taxa including low abundant taxa (“others”) across different diets. c Violin plots depicting alpha diversity indices of mycobiota composition in mice. The lines in the violin plot from bottom to top indicate 1st QR, median, and 3rd QR. The tips of the violin plot represent minima and maxima, and the width of the violin plot shows the frequency distribution of the data. d Beta diversity of intestinal fungi composition in mice displayed by canonical analysis of principal coordinates (capscale) plot of the BrayCurtis distances. e Differentially abundant mycobiota taxa identified by LEfSe algorithm in CAL (blue) and WES (red) mice. The root denotes the fungal ___domain and size of each node corresponds to the relative abundance of the taxon. f Heatmap showing fungal indicator species and mean scaled counts for every species within each diet. Statistical significance in panel b was determined using Kruskal–Wallis test followed by two-sided Mann–Whitney U test adjusted by FDR correction. In panel c statistical significance was determined using one-way ANOVA on residuals after sex and generation adjustment followed by Tukey’s multiple comparisons test. *Padj < 0.05, **Padj< 0.01, ***Padj< 0.01. Data in panel d was analyzed using “anova.cca” function (999 permutations) followed by “MANOVA.RM” for post hoc analysis. Source data for b–f are provided as a Source Data file.
