Ruth E. Ley
Associate Professor
Ruth E. Ley


Fax: 607-255-3904


Department of Microbiology
465 Biotechnology Building
Cornell University
Ithaca, NY 14853


Web Sites

Department Profile

Lab Website


Ruth Ley earned a B.A. in Integrative Biology from the University of California Berkeley. Her graduate training was at the University of Colorado Boulder with Steven Schmidt. Dr. Ley was an NRC Post-Doctoral Research Associate with Norman Pace at the University of Colorado, Boulder from 2001-2004. Her post-doctoral training continued with Jeffrey Gordon at Washington University School of Medicine’s Center for Genome Science from 2004-2007. She was an Assistant Research Professor in the Department of Developmental Biology at Washington University School of Medicine from 2007-2008 and joined the Cornell faculty in the Fall of 2008.

Research Description

Humans, like other animals, are born germ-free. However, once born, we are rapidly colonized with microbial cells that outnumber our own eukaryotic cells 10 to 1. The largest assemblage of microbes resides in the gut, where densities can approach 1012 cells/mL. The collective genome (microbiome) of our microbial partners complements and enhances our primate genome: we depend on our microbial partners for essential services such energy harvest from food and its detoxification, supplying vitamins, and protection against harmful invaders of our body surfaces. Although the human genome has been sequenced, characterization of the microbiome is just beginning. Surveys of the microbial lineages that form the microbiome (by 16S rRNA analysis) are becoming more extensive, and metagenomic analyses are revealing its functions.

Research in the Ley laboratory will address basic questions about human evolution in the microbial world: How has the microbiome co-evolved with its animal host species? How do host genetics relate to the structure of gut microbial communities? Does its composition make the host more or less predisposed to disease? To answer these questions requires data derived from an integration of high throughput sequencing technology such as pyrosequencing with experimental approaches.

Selected Publications

  • Turnbaugh, P.J., M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J. Jones, B.A. Roe, J.P. Affourtit, M. Egholm, B. Henrissat, A.C. Heath, R. Knight and J.I. Gordon. 2009. A core gut microbiome in obese and lean twins. Nature 457:480-484.
  • Wen*, L, R. Ley*, P. Volchkov*, P. Stranges, L. Avanesyan, A. Stonebraker, C. Hu, F.S. Wong, G.L. Szot, J.A. Bluestone, J.I. Gordon and A.V. Chervonsky. 2008. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455:1109-1113.
  • Ley*, R.E., C.A. Lozupone*, M. Hamedy, R. Knight and J.I. Gordon. 2008. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Reviews Microbiology 6:776-788.
  • Ley, R.E., M. Hamady, C. Lozupone, P.J. Turnbaugh, R.R. Ramey, J.S. Bercher, M.L. Schlegel, T.A. Tucker, M.D. Schrenzel, R. Knight and J.I. Gordon. 2008. Evolution of mammals and their gut microbes. Science 320: 1647-1651.
  • Ley, R. E., R. D. Knight and J. I. Gordon. 2007.The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.Environmental Microbiology 9: 3-4.
  • Turnbaugh, P. J., R. E. Ley, M. Mahowald, V. Magrini, E. R. Mardis, and J. I. Gordon. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
  • Ley, R. E., P. Turnbaugh, S. Klein and J. I. Gordon.2006.Human gut microbial ecology linked to obesity.Nature 444: 1022-1023.
  • Ley, R.E., D. A. Peterson and J. I. Gordon. 2006.An extended view of ourselves: ecological and evolutionary forces that shape microbial diversity and genome content in the human intestine. Cell 124: 837-848.
  • Ley, R.E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. Sogin and N. R. Pace.2006.Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 72: 3685-3695.
  • Rawls, J. F., M. M. Mahowald, R. E. Ley and J. I. Gordon. 2006.Reciprocal transplantation of gut microbial communities from zebrafish and mice into gnotobiotic recipients reveals host habitat selection of a microbiota. Cell 127: 423-433.