Meta-analysis reveals reproducible rapamycin-induced shifts in the mouse gut microbiome

Rapamycin is a geroprotective compound that extends lifespan and is well characterised in systemic physiology. However, due to heterogeneous methodologies, its effects on the gut microbiome, an emerging regulator of ageing and health, remain poorly defined. Here, we systematically assessed these effects in mice using a harmonised meta-analysis workflow, reprocessing raw sequence data end-to-end. We conducted a harmonised meta-analysis of the gut microbiome using 16S rRNA gene amplicon data from three independent mouse studies (n = 54) spanning dietary and intraperitoneal rapamycin interventions with matched controls. All samples were uniformly processed using a standardised 16S rRNA bioinformatics workflow. Genus-level abundances were modelled using two complementary approaches: a per-study zero-inflated beta modelling framework with random-effects meta-analysis, and a batch-corrected linear modelling framework incorporating correction prior to meta-analysis. Dose-response meta-regression assessed whether rapamycin-associated changes scaled with dose (42-990 mg/kg), integrating presence and magnitude of effects across heterogeneous study designs. Rapamycin treatment induced reproducible shifts in specific taxa across studies, with a subset of core responders consistently altered regardless of dose. Among the core responders, Bacteroides increased (OR = 1.59, q = 0.042) and Muribaculum decreased (OR = 0.55, q = 0.042), each significant in both frameworks. Whereas Ruminococcus decreased (OR = 0.60, q = 0.089), it was significant in the batch-corrected framework, but only a trend in zero-inflated modelling. Dose-sensitivity analyses highlighted Lachnospiraceae as the most consistent dose-sensitive taxon, with other associations largely restricted to extreme doses. Functional pathway analysis revealed alterations in energy metabolism and microbial stress response. This harmonised meta-analysis highlights notable shifts in the gut microbiome connected to rapamycin across the examined studies, outlining potential core microbial signatures. These findings were observed within heterogeneous experimental contexts, and further validation in additional studies will be needed to confirm their generality.