The microbiome’s impact on the human host is widely acknowledged. Correlations between certain disease states and the composition of the microbiota have been shown in both humans and animal models, but we are still in the infancy when it comes to understanding causal relationships between microbial species and host metabolism, physiology and immunology. Though established more than 60 years ago, germ-free rodents are still, and now more than ever, important models for studying the effect of different microbial communities and the mechanisms involved in the host-microbiome crosstalk.
The rising era of translational microbiome research sets new requirements for our capabilities to transplant microbial communities into rodents and to ensure that the success of the transplantation is not only measured in which species are transferred to the recipient and their relative abundances, but also how the transplant interacts with the host and develops the immune system. We need to fully understand best practices for obtaining the desired result; ranging from procurement and storage of the microbial transplant, the transplantation process, to the characteristics of the recipient animal, the surrounding environment and husbandry practices. Here, the present state-of-the-art on the generation of gnotobiotic rodents for microbiome research will be reviewed.