In the Department of Microbiome Science we ask fundamental questions about the evolutionary origins of the human gut microbiome and how it influences host physiology and evolution. We have the following main areas of research: (1) evolution of the human gut microbiome and interplay with host genetics, (2) lipids in host-microbiome symbiosis, (3) microbiota-innate immune interactions, (4) ecology and evolution of host-associated methanogens, and (5) host phenotype effects of heritable microbiota. Please read the subsections for more on these topics along with representative papers from the lab in these areas.
Goodrich J. K., Davenport E. R., Clark A. G., Ley R. E.: The relationship between the human genome and microbiome comes into view. Annual Review of Genetics (2017).
Goodrich, J. K. , E. R. Davenport, M. A. Jackson, M. Beaumont, R. Knight, T. D. Spector, J. T. Bell, A. G. Clark, R. E. Ley. Genetic determinants of the gut microbiome assessed in UK Twins. Cell Host & Microbe 19:731-43. (2016)
Goodrich, J. K., E. R. Davenport, J. L. Waters, A. G. Clark and R. E. Ley. Cross-species comparisons of host genetic associations with the microbiome. Science 352: 532-535. (2016)
Goodrich, J. K., J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. D. Spector, A. G. Clark and R. E. Ley. Human genetics shape the gut microbiome. Cell 159: 789-799. (2014)
Cullender, T. C., B. Chassaing, A. Janzon, K. Kumar, C. Muller, J. J. Werner, L. T. Angenent, M. E. Bell, A. G. Hay, D. A. Peterson, J. Walter, M. Vijay-Kumar, A. T. Gewirtz and R. E. Ley. Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host & Microbe 14: 571-581. (2013)
DiRienzi, S. C., I. Sharon, K. C. Wrighton, O. Koren, L. A. Hug, B. C. Thomas, J. K. Goodrich, J. T. Bell, T. D. Spector, J. F. Banfield and R. E. Ley. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2:e01102 (2013)
Koren, O., J. K. Goodrich, T. C. Cullender, A. Spor, K. Laitinen, H. Backhed, A. Gonzalez, J. J. Werner, L. T. Angenent, R. Knight, F. Backhed, E. Isolauri, S. Salminen and R. E. Ley. Remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 1-11 (2012).