Panel A shows horizontal bar plots comparing the relative abundance of predicted metabolic pathways between non-cohoused wild type and Lingo4 knockout mice, where the x-axis represents relative abundance and the y-axis lists different metabolic pathways, with an additional right-side heatmap indicating log2 fold change. Panel B and C show scatter bar plots of the frequencies of ILC3s in the small intestinal lamina propria of wild type and Lingo4 knockout mice under different dietary conditions, where the x-axis represents diet groups (chow, high fat diet, low fiber, high fiber) and the y-axis represents percentage of ILC3s. Panel D shows a multidimensional scaling plot based on Bray–Curtis distances illustrating microbial composition following fecal microbiota transplantation, where the axes represent principal coordinate dimensions. Panel E and F show stacked bar plots of relative microbial composition at the genus level (E) and phylum level (F), where the x-axis represents samples or conditions and the y-axis represents relative abundance. Panel G shows a scatter plot with a fitted regression line illustrating the association of Proteobacteria abundance with time post fecal microbiota transplantation, where the x-axis represents days and the y-axis represents relative abundance. Panel H shows a box plot comparing Firmicutes abundance between genotypes, where the x-axis represents genotype (wild type and Lingo4 knockout) and the y-axis represents relative abundance.
Microbiota-dependent regulation of ILC3s in Lingo4-deficient mice (related to Fig. 3). (A) Functional pathway predictions generated using PICRUSt2 based on 16S rRNA gene sequencing of non-cohoused WT vs. Lingo4−/− mice. n = 4. (B and C) Frequencies of ILC3s in siLP of WT and Lingo4−/− mice fed with high-fat (B) or low- or high-fiber diets (C). Mean ± SEM, n = 3–4; representative of two experiments. (D) MDS plot of WT and Lingo4−/− mice after FMT based on Bray–Curtis distances. n = 4. (E and F) Relative abundances at genus (E) and phylum (F) levels from samples shown in D. n = 4. (G and H) Differential abundance analysis by MaAsLin2 following FMT: association of Proteobacteria with time post-FMT in Lingo4−/− mice (G); association of Firmicutes with genotype (WT vs. Lingo4−/−) (H). n = 4. (B and C) Statistical significance was assessed using one-way ANOVA with Tukey’s post hoc test. *P < 0.05; **P < 0.01. MDS, multidimensional scaling.