Fig. 4: Cohousing ameliorates gut transit deficit and disease in FD mice.

a, b Progressive changes in microbiome (a) and metabolome (b) diversity in FD mice compared to control mice when separately housed or cohoused (size of circles = number of mice sampled at each time; DPW = days post-weaning; dotted line represents p = 0.05). c Pathology score of FD mice when housed separately or cohoused with control mice. d Carmine red-based gut transit for each mouse group. Groups in dotted box were cohoused. n = a, 79 DPW separately housed: 10 FD (4 female, 6 male; 3 cages) vs. 3 control (female; 1 cage); 79 DPW cohoused: 9 FD (6 female, 3 male; 3 cages) vs. 12 control (7 female, 5 male; 3 cages); 179 DPW separately housed: 10 FD (5 female, 5 male; 2 cages) vs. 11 control (5 female, 6 male; 3 cages); 179 DPW cohoused: 13 FD (6 female, 7 male; 4 cages) vs. 21 control (7 female, 14 male; 5 cages); 279 DPW separately housed: 13 FD (6 female, 7 male; 4 cages) vs. 21 control (7 female, 14 male; 5 cages); 279 DPW cohoused: 13 FD (7 female, 6 male; 4 cages) vs. 8 control (5 female, 3 male; 2 cages). b 79 DPW separately housed: 25 FD (14 female, 11 male; 6 cages) vs. 29 control (18 female, 11 male; 7 cages) mice; 79 DPW cohoused: 9 FD (6 female, 3 male; 3 cages) vs. 11 control (6 female, 5 male; 3 cages); 179 DPW separately housed: 10 FD (6 female, 4 male; 3 cages) vs. 9 control (7 female, 2 male; 3 cages); 179 DPW cohoused: 13 FD (6 female, 7 male; 4 cages) vs. 21 control (7 female, 14 male; 5 cages); 279 DPW separately housed: 15 FD (9 female, 6 male; 4 cages) vs. 12 control (5 female, 7 male; 3 cages); 279 DPW cohoused: 13 FD (6 female, 7 male; 4 cages) vs. 20 control (7 female, 13 male; 5 cages). c, 30–129 DPW: 86 separately housed (60 female, 26 male; 18 cages) vs. 21 cohoused (13 female, 8 male; 5 cages); 130–229 DPW: 66 separately housed (47 female, 19 male; 14 cages) vs. 34 cohoused (13 female, 21 male; 8 cages); 230–329 DPW: 40 separately house (22 female, 18 male; 9 cages) vs. 34 cohoused (13 female, 21 male; 8 cages); d, 15 FD (12 female, 3 male; 3 cages) and 11 control (all female; 3 cages) mice separately housed; 9 FD (6 female, 3 male; 3 cages) and 10 control (7 female, 3 male; 3 cages) mice cohoused. PERMANOVA (a, separately housed, day 79, df = 1, R² = 0.1528, day 179, df = 1, R² = 0.1193, day 279, df = 1, R² = 0.1941; cohoused, day 79, df = 1, R² = 0.0799; day 179, df = 1, R² = 0.0706; day 279, df = 1, R² = 0.0807; b, separately housed, day 79, df = 1, R²=, day 179, df = 1, R²=, day 279, df = 1, R² = ; cohoused, day 79, df = 1, R²=; day 179, df = 1, R²=; day 279, df = 1, R²=); Welch’s two-sample t-testing with FDR correction (c, DPW 30–129, t-statistic = −2.7203, df = 13.018, difference between FD cohoused and separately housed mice = −1.8403, 95% confidence interval of difference between FD cohoused and separately housed mice = −3.3015 to −0.3790; DPW 130–229, t-statistic = −4.1497, df = 28.434, difference between FD cohoused and separately housed mice = −2.1185, 95% confidence interval of difference between FD cohoused and separately housed mice = −3.1635 to −1.0735; DPW 230–329, t-statistic = −3.7242, df = 20.515, difference between FD cohoused and separately housed mice = −2.2170, 95% confidence interval of difference between FD cohoused and separately housed mice = −3.4568 to −0.9772; d, FD cohoused vs. separately housed, t-statistic = −2.9745, df = 18.025, difference between group means = −1.1576, 95% confidence interval of difference between group means = −1.9751 to −0.3400; control cohoused vs. FD separately housed, t-statistic = −4.6345, df = 22.825, difference between group means = −1.4317, 95% confidence interval of difference between group means = −2.0710 to −0.7923; control separately housed vs. FD separately housed, t-statistic = −3.5146, df = 23.385, difference between group means = −1.0759, 95% confidence interval of difference between group means = −1.7087 to −0.4432).