Extended Data Fig. 3: Reversion of F1 phenotypes coincident with restoration of preconception paternal gut microbiota.
From: Paternal microbiome perturbations impact offspring fitness
(a) Body weights of F1 offspring derived from males exposed to nABX for 6wk (dysbiotic) and after 4 weeks recovery following nABX withdrawal (6wk + 4rec; still dysbiotic) and 8 weeks recovery (6wk + 8rec; recovered). The same males are used throughout the time course. p-value indicates nested (hierarchical) unpaired two-tailed t-test that calculates significance based on the number of treated males (fathers) rather than number of shown offspring. (b) QQ normality plots for F1 offspring body weights when sired by 6wk nABX (left), 6wk + 4rec (centre) or recovered 6wk + 8rec fathers (right). The plots indicate that SGR (low weight) offspring from dysbiotic fathers occur at a higher frequency than expected, indicating there is a change in the distribution (in addition to the mean) of F1 body weights, as indicated by excess kurtosis values. This implies a probabilistic affect that increases the frequency of outliers (SGR). (c) Volcano plot of gene expression in adipose of F1 offrpsing from 6wk + 4rec nABX fathers. Overlayed in green/ochre are differentially expressed genes from independent offspring derived from 6wk nABX fathers, indicating an equivalence in expression changes and directionality between cohorts sired from independent dysbiotic fathers. p-value adjusted for multiple testing. (d) Bubble plots showing gene ontology analysis of differentially expressed genes in F1 SGR offspring sired from 6wk or 6wk + 4rec fathers shows a striking similarity of enrichments. This suggests these independent dent offspring acquire a reproducible molecular response to paternal dysbiosis, whereas no SGR offspring were observed from 6wk + 8rec time points, indicating the effect is robust during the period of paternal gut microbiota perturbation but reverts coincident with recovery.
