Ruth Ley

Ruth Ley

Associate Professor

465 Biotech
(607) 255-4954

Ruth Ley received a BA in Integrative Biology from the University of California at Berkeley and a Ph.D at the University of Colorado at Boulder working with Dr. Steven Schmidt. She received a National Research Council NASA Astrobiology Fellowship for post-doctoral work on the microbial diversity of hypersaline microbial mats with Dr. Norm Pace. She then moved to Washington University School of Medicine to work with Dr. Jeffrey Gordon on the human microbiome. Dr. Ley joined the Department of Microbiology at Cornell University in 2008 and the Department of Molecular Biology and Genetics in 2014. Her awards include a Packard Fellowship, a Hartwell Fellowship, a Beckman Fellowship, the NIH Director’s New Innovator Award, the CALS Outstanding Accomplishments in Early Achievement Award and the International Society for Microbial Ecology's Young Investigator Award.

Research Focus

Host interactions with the microbiome are deeply implicated in modern metabolic plagues: metabolic syndrome, type 2 diabetes, and obesity. If we could better understand how the microbiome impacts host metabolism, we could address therapeutically an underlying driver of the biggest health problems that we face today.


Eukaryotic species have harnessed the microbiota to extend their phenotypes, yet gut microbiomes are immensely complex. When new hosts (infants) emerge, microbes are assembled into their microbiomes from the environment. The microbiome is challenged during disturbances, augmented by newly arriving microbes, and its residents are aided by their syntrophic partners. Host exudates including peptides, mucus, and antibodies, all have been implicated in shaping the composition of these communities. In turn the host can be irreversibly reliant on its microbiome for immune development, nutrient release, and a growing list of other aspects of metabolism. The specifics of the mix at any given time can have profound impacts on host metabolism and health.


The role of host genetic variation in shaping the microbiome remains to be discerned. In the Ley lab, we are broadly interested in how host genetics control the microbiome in the human gut. We explore how interactions between host genetic status and the microbiome influence host metabolic phenotypes. To do so, we employ genetics, genomics, metabolomics, gnotobiotics (ie, transplantation of microbes into germfree mice) and tools of mucosal immunology.

Teaching Focus

Human-associated microbes in health and disease.

Scientific Communication.
Graduate level course, taught Fall 2008. BioMI7970

Awards and Honors

  • International Society for Microbial Ecology (ISME) Young Investigator’s Award (2013)
  • Cornell University College of Agriculture and Life Sciences Research and Extension Award for Outstanding Accomplishments in Early Achievement (2011) Cornell University CALS
  • NIH Director’s New Innovator Award (2010) NIH

Selected Publications

Journal Publications

  • Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., & Ley, R. (2013). A guide to Enterotypes across the human body: A meta-analysis of microbial community structures in human microbiome datasets. PLoS Computational Biology. 9:e1002863.
  • Peiffer, J., Spor, A., Jin, Z., Koren, O., Tringe, S. G., Dangl, J. L., Buckler, E. S., & Ley, R. (2013). Diversity and heritability of the Maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences of the United States of America. 5:570-573.
  • Cullender, T. C., Chassaing, B., Janzon, A., Kumar, K., Muller, C., Werner, J. J., Angenent, L., Bell, M. E., Hay, A. G., Peterson, D. A., Walter, J., Vijay-Kumar, M., Gewirtz, A. T., & Ley, R. (2013). Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe. 14:571-581.
  • DiRienzi, S. C., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., Goodrich, J. K., Bell, J. T., Spector, T. D., Banfield, J. F., & Ley, R. (2013). The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife. 2:e1102.
  • Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrekston, A., Kunin, V., del Rio, T. G., Edgar, R., Eickhorst, T., Ley, R., RP. Hugenholtz, S. T., & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome.. Nature. 486:207-214.
  • Koren, O., Goodrich, J. K., Cullender, T. C., Spor, A., Laitinene, K., Backhed, H., Gonzalez, A., Werner, J. J., Angenent, L., Knight, R., Backhed, F., Isolauri, E., Salminen, S., & Ley, R. (2012). Remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 150:1-11.
  • Dominguez-Bello, M. G., Blaser, M. J., Ley, R., & Knight, R. (2011). Development of the infant gut microbiota: insights from high-throughput sequencing. Gastroenterology. 140:1713-1719.
  • Vaishnava, S., Yamamoto, M., Severson, K. A., Ruhn, X., Yu, O., Koren, R. E., Ley, R., Wakeland, L., & Hooper, V. (2011). The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science. 334:255-258.
  • Walter, J., & Ley, R. (2011). The human gut microbiome: ecology and recent evolutionary changes. Annual Reviews of Microbiology. 65:411-429.
  • Spor, A., Koren, O., & Ley, R. (2011). Unraveling the effects of environment and host genotype on the gut microbiome. Nature Reviews Microbiology. 9:279-290.