Fig. 2

Effect of antibiotics and cohousing on the gut microbiota. SOD1 and WT littermates were treated with antibiotics, cohoused, or did not receive treatment (H₂O) n = 11–13 per group. Microbiota samples were collected at day 30 of life (baseline), then at days 37, 51, and 93, and 121. a ADONIS test of microbiota samples. Treatment, timepoint, and cage have a substantial contribution to microbiome variation, whereas strain (WT vs. SOD1) has no effect. ***p=0.001 b Principal coordinate analysis of unweighted UniFrac distances show that samples cluster at baseline and are shifted by antibiotic treatment, but not genotype or cohousing. c Microbiota divergence from baseline as measured by unweighted UniFrac distances. d Microbiota composition over time shows expansion of Ralstonia, Streptococcus, and Weisella. e Genera altered by antibiotics that were significant at ≥ 3 timepoints, *p <0.05, **p < 0.01, ***p < 0.001, linear discriminant analysis effect size. f Select genera decreased or increased by antibiotic treatment. Statistics shown in panel e for LEfSe and in Supplementary Table 1 for pairwise UniFrac distances (c)