Exploratory multi-omics analysis reveals sex-specific differences in microbial response to antibiotic exposure

Antibiotic exposure is a major driver of microbiome disruption and antimicrobial resistance gene (ARG) expansion. Yet, the role of biological sex in shaping these responses remains poorly understood. Most studies do not stratify antibiotic-induced microbiome changes by sex or integrate multi-omics datasets, limiting our understanding of how microbial, metabolic, and immune responses interact. Therefore, there remains a critical need for an integrative systems-level approach to determine how sex-specific disruptions under antibiotic pressure are paralleled across microbial, metabolic, and host immune layers. The objective of this work was to perform an exploratory study investigating how continuous antibiotic exposure reshaped the gut microbiome across sexual maturation and how these perturbations influenced downstream host responses in a sex-specific manner using an integrative multi-omics framework. Male and female mice that were exposed to continuous antibiotics were profiled over sexual maturation using shotgun metagenomics, untargeted metabolomics, and bulk RNA sequencing of the spleen to assess microbial composition, ARG dynamics, metabolic profiles, and immune responses. Overall, our results demonstrated sex-specific correlations at a systems-level that help provide valuable context to the differences observed in males and females upon antibiotic exposure.