The gut microbiota operates at the interface of host-environment interactions to influence human homoeostasis and metabolic networks^(1-4). Environmental factors that unbalance gut microbial ecosystems can therefore shape physiological and disease-associated responses across somatic tissues^(5-9). However, the systemic impact of the gut microbiome on the germline-and consequently on the F(1) offspring it gives rise to-is unexplored^(10). Here we show that the gut microbiota act as a …