Extended Data Fig. 4: No evidence for increased structural or nucleotide variants in F1 offspring or transgenerational F2 phenotypes.
From: Paternal microbiome perturbations impact offspring fitness
(a) Analysis of structural variants in independent F1 offspring sired by control or nABX-treated fathers reveals no change in their frequency irrespective of father’s status or offspring phenotype (normal or severe growth restriction: SGR). Each bar is an independent F1 offspring. (b) Analysis of nucleotide variants amongst independent F1 offspring from control or nABX fathers, showing no change in their frequency. These data indicate that the SGR F1 phenotype derived from nABX fathers is not associated with any increased rate of genetic abnormalities. We also did not identify any coding mutations underlying SGR phenotype. Note, most identified indels are ‘common’ (present in n = 6 (all) offspring), or ‘uncommon’ (present in n = 2–5 offspring), indicating they represent baseline nucleotide polymorphisms inherent throughout our C57BL/6J mouse colony relative to the reference genome. (c) Schematic showing the experimental design. Control or nABX-treated F0 males were mated with naive females and their F1 offspring were intercrossed to examine potential F2 effects. Note, the subset of F1 offspring with a severe growth restriction (SGR) phenotype could not be intercrossed, as they typically exhibited mortality prior to sexual maturity. Because of this reason and irrespective of F2 phenotype, nABX-exposed F0 males are predicted to have reduced F2 (transgenerational) fitness, as judged by number of grand-progeny. This reflects fewer sexually mature F1 offspring, which in turn would produce fewer F2 in absolute terms. (d) Dot plot showing neonatal (P3) and post-weaning (P21) body weight of F2 offspring is not altered (F2 n = 39 offspring from 6 intercrossed F1 CON offspring, F2 n = 50 offspring from 10 intercrossed F1 nABX offspring). Significance by nested two-tailed t-test. (e) Growth curves of all F2 offspring from grandpaternal control or nABX conditions (CON n = 39 F2 (6 litters); nABX n = 50 F2 (10 litters)). Significance by nested two-tailed t-test. (f) Survival plot of F2 offspring. Significance by Mantel–Cox test (log-rank). n = number of F2 offspring, N = number of independent F1 parents.
