Antimicrobial regime for gut microbiota depletion in experimental mice models

Mice models serve as a valuable tool to study microbiome-immune system interactions. While the use of germ-free mice may represent the gold-standard method, antibiotic-based microbiome depletion provides a more cost-efficient and feasible system. The protocol here in presented provides a mild antimicrobial regime to deplete basal microbiota in 8-week-old C57BL/6 mice, aiming to ensure reproducibility in microbiota studies. The antibiotic regime combines five different antimicrobial agents delivered either ad libitum or via oral gavage, aiming at depleting core gut microbiota in mice. Various administration timings were explored, concluding there were no differences when the antimicrobial treatment was applied for 3, 5 or 7 consecutive days. By offering a detailed antimicrobial preparation and mouse administration, as well as fecal sample processing and 16s rRNA sequencing, this protocol provides an initial framework to develop mice microbiota studies, with perceptible results in fecal microbiota composition.