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Int J Med Microbiol. 2016 Aug;306(5):316-327. doi: 10.1016/j.ijmm.2016.03.002. Epub 2016 Mar 5.

The mouse gut microbiome revisited: From complex diversity to model ecosystems.

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ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany. Electronic address:
ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany.
Department of Gastrointestinal Microbiology, German Institute of Human Nutrition (DIfE), Nuthetal, Germany.
Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany. Electronic address:


Laboratory mice are the most commonly used animal model in translational medical research. In recent years, the impact of the gut microbiota (i.e. communities of microorganisms in the intestine) on host physiology and the onset of diseases, including metabolic and neuronal disorders, cancers, gastrointestinal infections and chronic inflammation, became a focal point of interest. There is abundant evidence that mouse phenotypes in disease models vary greatly between animal facilities or commercial providers, and that this variation is associated with differences in the microbiota. Hence, there is a clear discrepancy between the widespread use of mouse models in research and the patchwork knowledge on the mouse gut microbiome. In the present manuscript, we summarize data pertaining to the diversity and functions of the mouse gut microbiota, review existing work on gnotobiotic mouse models, and discuss challenges and opportunities for current and future research in the field.


Anaerobic cultivation; Bacterial diversity; Gnotobiology; Host–microbe interactions; Minimal microbiome; Mouse intestinal microbiota

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