The role of the gut microbiota on animal model reproducibility

The gut microbiota is composed of approximately 10(10)‐10(14) cells, including fungi, bacteria, archaea, protozoa, viruses, and bacteriophages; their genes and their various metabolites were found throughout the gastrointestinal tract. It has co‐evolved with each species to assist with day to day bodily functions, such as digestion, metabolism of xenobiotics, development of mucosal immunity and immunomodulation, and protection against invading pathogens. Because of the significant beneficial impact that gut microbiota may have, there is interest in learning more about it and translating these findings into clinical therapies. Results from recent studies characterizing the gut microbiota of various species have demonstrated the range of influences that may affect gut microbiota diversity, including animal strain, obesity, types of enrichment used, bedding and housing methods, treatment with antimicrobials, vendor source, specific animal housing, diet, and intercurrent disease. Relatively little is known about the functional consequences of alterations of the gut microbiota and exactly how changes in richness and diversity of the microbiota translate into changes in health and susceptibility to disease. Furthermore, questions have been raised as to whether germ‐free or even ultraclean, barrier‐raised mice are relevant models of human disease, given their significantly reduced gut microbiota diversity and complexity compared with conventionally housed mice. In addition, evidence suggests that the specific anatomical location selected for assessing the gut microbiota has a highly significant effect on study outcomes, in that bacterial phyla change significantly along the gastrointestinal tract. This paper will explore animal model reproducibility in light of this information about the gut microbiota.