Studies investigating whether there is a causative link between the gut microbiota and lifespan have largely been restricted to invertebrates or to mice with a reduced lifespan because of a genetic deficiency. We investigate the effect of early-life antibiotic exposure on otherwise healthy, normal chow-fed, wild-type mice, monitoring these mice for more than 700 days in comparison with untreated control mice. We demonstrate the emergence of two different low-diversity community types, post-antibiotic microbiota (PAM) I and PAM II, following antibiotic exposure. PAM II but not PAM I mice have impaired immunity, increased insulin resistance, and evidence of increased inflammaging in later life as well as a reduced lifespan. Our data suggest that differences in the composition of the gut microbiota following antibiotic exposure differentially affect host health and longevity in later life. Display omitted •Analysis of aged mice exposed to antibiotics in the pre-weaning period•Microbiota community type following antibiotics affects host health in later life•PAM II mice have increased insulin resistance, inflammaging, and reduced lifespan Lynn et al. expose mice to antibiotics in early life and then monitor these mice for more than 700 days. The study reveals that differences in the composition of the gut microbiota following antibiotic exposure differentially affects host immunity, metabolism, and longevity in later life.