Standardization in host–microbiota interaction studies: challenges, gnotobiology as a tool, and perspective

•Host–microbiota interaction studies require standardization.•Gnotobiology as a tool to standardize murine research models.•Overview, advantages and limitations of gnotobiotic models of different complexity.•Strategies to monitor hygiene status in axenic and gnotobiotic animals. Considering the increasing list of diseases linked to the commensal microbiota, experimental studies of host–microbe interactions are of growing interest. Axenic and differently colonized animal models are inalienable tools to study these interactions. Factors, such as host genetics, diet, antibiotics and litter affect microbiota composition and can be confounding factors in many experimental settings. The use of gnotobiotic mice harboring defined microbiotas of different complexity plus additional housing standardization have thus become a gold standard to study the influence of the microbiome on the host. We highlight here the recent advances, challenges and outstanding goals in gnotobiology with the ambition to contribute to the generation of reliable, reproducible and transferrable results, which form the basis for advances in biomedical research.