Jonathan B. Clayton


The Clayton lab is studying host-microbiome interactions in humans and nonhuman primates. We are using nonhuman primates as a model for studying the effects of variations in dietary fiber and other dietary compounds, as well as lifestyle factors associated with modernized society, on the microbiome and metabolic health. Dr. Clayton received his Doctor of Veterinary Medicine (D.V.M.) and his Doctor of Philosophy (Ph.D.) in Comparative and Molecular Biosciences from the University of Minnesota. For his Ph.D. thesis research, he used nonhuman primates as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. During his Ph.D., Dr. Clayton founded the Primate Microbiome Project (PMP) with the intended purpose to develop a systematic map of variation in microbiome structure and function across all primates and to relate this to primate health, evolution, behavior, and conservation. The Clayton Lab are currently extending our research to explore in detail causal mechanisms for microbiome-modulated metabolic diseases including diabetes and obesity, as well as neurological/behavioral diseases such as stress. We do this using both in vitro and in vivo experiments, including, but not limited to, next-generation sequencing, anaerobic and aerobic culture, germ-free mouse models, and marmoset models.

Featured Publications

Clayton JB, Al-Ghalith GA, Long HT, Van Tuan B, Cabana F, Huang H, Vangay P, Ward T, Van Minh V, Tam NA, Nguyen TD. Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model. Scientific Reports (Nature Publisher Group). 2018 Jul 1;8:1-6.


Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE. The gut microbiome of nonhuman primates: Lessons in ecology and evolution. American journal of primatology. 2018;80:e22867.


Clayton J. B., Johnson, T. J., Huang, H., Vangay, P., Ward, T., Travis, D. A., Ha, L. T., Bui, T. V., Vo, M. V., Glander, K. E., and Knights, D. (2016). Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences, 113(37), 10376–10381.


Gohl, D. M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T., Clayton, J. B., Johnson, T. J., Hunter, R., Knights, D., and Beckman, K. B. (2016). Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology, 34(9), 942-949.