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Sex outcome and maternal investment in progeny are important predictors of reproductive success. While environmental factors appear to influence these processes, there is little evidence to date of a direct role for gut commensals. Here we show that the reproductive outcomes (sex and survival) of mouse litters depend on signals conveyed through the microbiome. We discover that transient treatment of mouse mothers with specific microorganisms increases the absolute survival of offspring and skews offspring sex ratios via an endocrine-dependent mechanism requiring the neurophysiological hormone oxytocin. The implication of maternal oxytocin levels suggests that commensal microbes may have a broad role in modulating host endocrine and neurological pathways.