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Gut microbiome (GM), the complex community that combines all bacteria, viruses, protozoa, and fungi located in the gut of human or animal, plays a significant role in host health and disease. Animal model are widely used to investigate human disease in biomedical research. The GM differs in animal models results from many factors such as vendors, facilitates, husbandry, environment, etc. The variation of GM can contribute to the difference of the disease phenotype in animal models which results in poor reproducibility and repeatability in biomedical research. The differences in the gut virome can also impact the repeatability between animal models and contribute to the poor translatability of animal disease models to human disease due to less pathogen exposure in lab animals. The different methods of GM modulation also can lead to differences between animal models of disease. In this project, first, we investigated the potential contributors to research repeatability and translatability of animal models by characterizing the gut virome differences between mice from different sources including pet stores and different laboratories. Second, we assessed the role of differing GM transfer methods of efficiency and completeness of transfer of GM and impact of transfer on the DSS model of colitis. Ultimately to explore and provide a better way for the biomedical research community to do the GM transfer with higher transfer efficiency and more practical in any genetically modified animal disease model with desired GM. We applied the gold standard GM transfer method, embryo transfer (ET), to assess the genetic background and GM contributing to the GM transfer efficiency and subsequent disease phenotype in animal model. We transferred well-established richness GM4 and low richness GM1 to two different substrain B6J and B6N mice to assess the GM and genetic influence on the recipient mice and the subsequent influence on disease phenotype in DSS-induced chronic colitis mouse model. We found that both GM and substrain genetic background contributing to the GM transfer efficiency and have an influence on the disease phenotype in mouse models. We then designed experiments using the same GM transfer to the same genetic background recipient mice to compare and investigated the different transfer methods (standard ET, commonly used co-house, and newly explored cross-foster) influence on GM transfer efficiency in animal models and subsequent influence on disease phenotype. In conclusion, by comparing the gut virome of standard lab mice and presumably more antigen-experienced wild and pet store mice we explored how informative and translational standard lab mice are in contemporary biomedical research and by comparing the gut virome of mice from different vendors the project addressed one of the possible causes of poor reproducibility in biomedical research that uses mice. We investigated and determined whether differing GM transfer methods and the associated differences in GM transfer efficiency result in differences in animal model phenotypes using the DSS model of colitis. We also established efficient and economically feasible methods of GM transfer that can be applied to any genetically engineered mouse model of disease. Cross-foster could be used as an alternate GM transfer method to transfer the same desired GM to an animal model if the gold standard ET is not available in the lab. The result generated using co-house method as a GM-associated modulation manner should be interpreted with caution.

The influence of host genetics, virome, and gut microbiota transfer methods in mouse model reproducibility