The pioneering studies on new animal models for gut microbiota research have greatly demonstrated their potential. However, despite the limitations of mouse models, their advantages are numerous and, furthermore, the amount of research and knowledge on mouse gastroenterology, genetics and immunology far surpasses any other model. Murine mouse models provide a range of customizable genotypes and phenotypes far superior to any other model organism. They have thus played a very important role in the emerging gut microbiota research field. Owing to their widespread use in biomedical research, these models are complemented with extensive knowledge on genetic background and deep phenotypic and functional characterization. Moreover, with well-set-up standardized mouse house facilities throughout labs in the world, conducting experiments on mouse models, even germfree ones, can be more easily achieved than with other models.
Each one of the animal models shows some similarity to the physiology of the human digestive system, thus providing useful knowledge from different angles about the gut microbiota in health and disease. It is clear that information obtained from studies using alternative models has diversified our understanding of the mammalian gut microbiota in general and has deepened our knowledge of each model separately. It is, however, important to keep in mind that models always have some degree of dissimilarity with the system modeled. Therefore, results from animal models, including the popular murine ones, are not always translatable to humans and conclusions should be made with caution. In addition, even well-controlled gut microbiota experiments using mouse models show important inter-study variations due to confounding factors in the experimental setup, such as mouse house origin, maternal effects, environmental conditions (food composition, light, stress factors, pathogen infection), genetic backgrounds and in the downstream analysis methods applied.
There have been recent efforts to standardize gut microbiota experiments, for example by establishing standardized microbiota in isobiotic mice that would be shared by institutions involved in gut microbiota research (Hooper et al., 2012). Although these efforts are still in their infancy (Würbel, 2000), they will increase result reproducibility and inter-study comparability, and allow for the healthy growth of the gut microbiota research field.