Improving “mice with natural microbiota” model through controlled microbial exposure

Laboratory-raised specific pathogen-free (SPF) mice have been indispensable for fundamental scientific research, yet their reliability in predicting human clinical outcomes has been questionable. A major factor contributing to this disconnect is the sanitized housing environment, which deprives laboratory mice of physiological microbial exposure critical for immune maturation. Various approaches have been developed to introduce microbes to SPF mice, aiming to mimic human-like microbial experiences and engender adult human-like immune traits. However, many of these methods suffer from significant variability in pathogen exposure and mortality, driven by the uncontrolled nature of microbial exchange. Here we present a simple gavage-fomite (GaF) method that provides controlled exposure to a diverse array of pathogens and commensal while limiting mortality. GaF-treated mice exhibited consistent microbial exposure histories, robust immune maturation characterized by mucosal T-cell distribution and elevated serum inflammatory cytokines, and a systemic immune transcriptional signature closely aligned with that of adult humans. Furthermore, these mice demonstrated enhanced protection against a virulent bacterial challenge. The improved reproducibility, simplicity and effectiveness of the GaF method provides a valuable tool for generating “mice with natural microbiota”, enabling widespread adoption and advancement of both basic and translational research across institutions.