Networks
Ley, Ruth E.
Cornell Faculty Member
Close
Positions
- Assistant Professor, Microbiology (BIOMI), College of Agriculture and Life Sciences (CALS)
- Assistant Adjunct Professor, Molecular Biology and Genetics (MBG), College of Agriculture and Life Sciences (CALS)
Ruth Ley received a BA in Integrative Biology from the University of California at Berkeley and worked for 3 years on the Big Island of Hawaii on plant ecosystem processes. Her graduate work at the University of Colorado at Boulder with Dr. Steven Schmidt focused on the microbial processing of atmospheric nitrogen by soil microbes in high altitude talus soils. She received a National Research Council NASA Astrobiology Fellowship to 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. In 2008 Ley joined the Department of Microbiology at Cornell University as an Assistant Professor. Her awards include a Packard Fellowship, a Hartwell Fellowship, a Beckman Fellowship, and the NIH Director’s New Innovator Award.
Websites
- Affiliations
- Research
- Publications
- Teaching
- Service
- Background
- Other
- View All
Affiliations
other Cornell affiliations
Research
research overview
- Humans, like other animals, are born germ-free. However, once born, we are rapidly colonized with microbial cells that outnumber our own eukaryotic cells by 10 to 1. The largest assemblage of microbes resides in the gut, where densities can approach 1012 cells/mL. The collective genomes of our microbial partners complement and enhance our primate genome: we depend on our microbial partners for essential services such energy harvest from food, its detoxification, a supply of vitamins, and protection against harmful invaders. In the Ley laboratory we are interested in what factors shape the composition of the gut microbiota, and how the composition of gut microbiota translates into services (or disservices) to the host. We are applying the principles of ecosystem ecology to the gut microbiota, to ask how diversity and microbial community structure impact ecosystem processes such as decomposition of the diet (digestion efficiency), stability (resistance to invaders), and resilience (resistance to stress). We use mice as model replicate ecosystems. The goal of our animal studies is to establish basic principles that can be used to guide studies of human diseases where the gut microbiota are implicated. Therefore, we also team up with clinicians to search for links between the composition of the gut microbiota and disease in humans: we are currently working on studies of type 1 diabetes, metabolic syndrome, and HIV.
principal investigator on
- ADAPTIVE IMMUNE RESPONSES TO GUT BACTERIA IN THE TEDDY COHORT awarded by NATL INST OF DIABETES, DIGESTIVE & KIDNEY, NIH 2010 - 2012
- COLLABORATIVE RESEARCH: MSB: DEFINING PLANT ASSOCIATED METAGENOMICS awarded by NATL SCIENCE FOUNDATION 2010 - 2014
- DEFENSIN REGULATION OF HUMAN GUT MICROBIAL COMMUNITIES awarded by BECKMAN FOUNDATION 2009 - 2012
- DEVELOPMENT OF IMMUNIZATION STRATEGIES TO RESHAPE PATHOGENIC MICROBIOMES awarded by NATL INST OF GENERAL MEDICAL SCIENCES, NIH 2010 - 2015
- GENETIC TRANSMISSION OF COMPONENTS OF THE HUMAN GUT MICROBIOME awarded by NATL INST OF HEALTH DHHS 2011 - 2015
- HOST-MICROBIAL INTERACTIONS UNDERLYING STARCH UTILIZATION AND BODY WEIGHT awarded by GENERAL MILLS BELL INSTITUTE OF HEALTH AND NUTRITION 2010 - 2013
- PACKARD FOUNDATION FELLOWSHIP awarded by DAVID & LUCILE PACKARD FND 2011 - 2015
co-principal investigator on
- FUNCTIONAL ANALYSIS OF CROHN'S ASSOCIATED ADHERENT AND INVASIVE E. COLI awarded by CROHN'S & COLITIS FDN OF AMERICA 2011 - 2013
- MICROBIOMES AND INFLAMMATION IN CHRONIC FATIGUE SYNDROME awarded by NATL INST OF HEALTH DHHS 2012 - 2014
area(s) of concentration/expertise
keywords
- host-microbial interactions
- human microbiome
- microbiology
Publications
individual publications
-
academic article
- A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS Computational Biology. 9. 2013
- A framework for human microbiome research. Nature. 486:215-221. 2012
- Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut. 61:1124-1131. 2012
- Defining the core Arabidopsis thaliana root microbiome.. Nature. 488:86-90. 2012
- Host remodeling of the gut microbiome and metabolic changes during pregnancy.. Cell. 150:470-480. 2012
- IL-1β promotes susceptibility of Toll-like receptor 5 KO mice to colitis. Gut. 61:373-384. 2012
- Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys.. International Society for Microbial Ecology Journal. 6:94-103. 2012
- Integrated and novel survey methods for rhinoceros populations confirm the extinction of Rhinoceros sondaicus annamiticus from Vietnam.. Biological Conservation. 155:59-67. 2012
- Responses of gut microbiota to weight loss in obese and lean mice. Obesity. 20:738-747. 2012
- Transient inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.. Cell Host Microbe. 12:139-152. 2012
- Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys. The ISME Journal. 2011
- Branched chain fatty acids reduce the incidence of necrotizing enterocolitis in a neonatal rat model and alter gastrointestinal microbial ecology. PLoS One. 6. 2011
- Development of the infant gut microbiota: insights from high-throughput sequencing. Gastroenterology. 140:1713-1719. 2011
- Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences of the United States of America. 108:4578-4585. 2011
- The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science. 334:255-258. 2011
- The human gut microbiome: ecology and recent evolutionary changes. Annual Reviews of Microbiology. 65:411-429. 2011
- Unraveling the effects of environment and host genotype on the gut microbiome. Nature Reviews Microbiology. 9:279-290. 2011
- Direct sequencing of the human microbiome readily reveals community differences. Genome Biology. 5:210-219. 2010
- Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science. 328:228-231. 2010
- Obesity and the human gut microbiome. Current Opinion in Gastroenterology. 26:5-11. 2010
- QIIME allows integration and analysis of high-throughput community sequencing data. Nature Methods. 7:335-336. 2010
- Supervised classification of microbiota mitigates mislabeling errors. International Society for Microbial Ecology Journal. 5:570-573. 2010
- A core gut microbiome in obese and lean twins. Nature. 457:480-484. 2009
- Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird. Applied and Environmental Microbiology. 74:1647-1651. 2008
- Evolution of mammals and their gut microbes. Science. 320:1647-1651. 2008
- Host-bacterial coevolution and the search for new drug targets. Current Opinion in Chemical Biology. 12:109-114. 2008
- Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature. 455:1109-1113. 2008
- Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Reviews Microbiology. 6:776-788. 2008
- Eucaryotes in the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology. 74:329-332. 2007
- Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology. 5. 2007
- The human microbiome project. Nature. 449:804-810. 2007
- The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology. Environmental Microbiology. 9:3-4. 2007
- An extended view of ourselves: ecological and evolutionary forces that shape microbial diversity and genome content in the human intestine. Cell. 124:837-848. 2006
- An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 444:1027-1031. 2006
- Microbial ecology: human gut microbes associated with obesity. Nature. 444:1022-1023. 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. 2006
- The human intestinal microbiota and its relationship to energy balance. Scandinavian Journal of Food and Nutrition. 50:121-123. 2006
- Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology. 72:3685-3695. 2006
- Host-bacterial mutualism in the human intestine. Science. 307:1915-1920. 2005
- Obesity alters gut microbial ecology. Proceedings at the National Academy of Science USA. 31:11070-11075. 2005
- Microbial population dynamics in an extreme environment: controlling factors in unvegetated talus soils at 3750m in the Colorado Rocky Mountains. Biogeochemistry. 68:313-335. 2004
- Soil microbial dynamics in Costa Rica: seasonal and biogeochemical constraints. Biotropica. 36:184-195. 2004
- The impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils. Biogeochemistry. 69:1-17. 2004
- Sub-freezing activity of microorganisms and the potential habitability of Mars' polar regions. Astrobiology. 3:343-351. 2003
- Alteration of ecosystem nitrogen dynamics by exotic plants: a case study of C4 grasses in Hawai'i. Ecological Applications. 11:1323-1335. 2002
- Fungal and bacterial responses to amino acid and phenolic compound additions in high altitude barren soil. Soil Biology and Biochemistry. 34:989-995. 2002
- Microbial biomass levels in high elevation vegetated and barren talus soils. Soil Science Society of America Journal. 65:111-117. 2001
- Soil ecological interactions: comparisons between tropical and subalpine forests. Oecologia. 128:549-556. 2001
- Alien plant invasions decrease potential rates of nitrogen fixation in dry tropical forests of Hawai'i. Oecologia. 113:179. 1998
-
article
-
chapter
- The human intestinal microbiota and microbiome. Textbook of Gastroenterology, Fifth edition. 2011
- The human intestinal microbiota and microbiome. Textbook of Gastroenterology. 635. 2009
- Microbial competition and soil structure limit the expression of allelochemicals in nature. Allelopathy: Procedures and Processes. 339-351. 1999
-
document part
- Evolution of the human microbiome 2009
- Integrating host genetics and environment in interpreting the microbiota 2009
- An evolutionary perspective on obesity. 2008
- Analysis of distal gut in adults 2007
- Evolutionary ecology of the mammalian gut microbiota. 2006
- Microbial diversity of our inner selves. 2005
- A molecular view into hypersaline microbial mat communities: vast diversity, unexpected composition, discrete structure. 2004
- A molecular view into hypsersaline microbial mat communities: vast diversity, unexpected composition, discrete structure 2004
- Enrichment of Hydrogen-utilizing Microorganisms from Hypersaline Microbial Mats with a Hollow-fiber Bioreactor 2004
- Enrichment of Hydrogen-utilizing Microorganisms from Hypersaline Microbial Mats with a Hollow-fiber Bioreactor 2004
- Identification of symbionts in hypersaline microbial mats 2003
- Green Non Sulfur bacteria dominate the photic zone of cyanobacterial mats at Guererro Negro, Baja CA. Sur, Mexico. 2002
- High diversity of Bacteria in hypersaline mats at Guererro Negro, Baja CA. Sur, Mexico 2002
- Microbial diversity of a hypersaline microbial mat. 2002
- Specific microbes respond during substrate-induced respiration (SIR, SIGR) assays in soil 2001
- Seasonal changes in microclimate and microbial populations in high elevation talus soils 2000
- Microbial functional group characteristics along an organic matter gradient in talus soils at 4000m in the Colorado Rocky Mountains 1999
- Biogeochemical diversity and growth of microbial communities in cold, unvegetated soils of Rocky Mountain talus fields (4000 m) 1998
- Microbial community composition and activity in talus soils from above 3500m 1997
- Fire effects on N-fixation rates in a seasonally dry Hawai'ian woodland 1995
- Distribution of algae on the barrier reef crest of Moorea, French Polynesia 1991
- Extending our view of self: the human gut microbiome initiative (HGMI) 2005
presentations
featured in archived article
Teaching
teaching overview
- Human-associated microbes in health and disease. Scientific Communication. Graduate level course, taught Fall 2008. BioMI7970
teaching activities
Service
service to the profession
- New York Academy of Science Member 2009 -
- The Rare Biosphere Colloquium Participant - 2009
- International Society for Prebiotics and Probiotics Group Co-Chair - 2009
- ISS Congress Session Chair - 2009
- German-American Frontiers of Science Chairperson 2008 - 2009
- German-American Frontiers of Science Symposium Program Organizer - 2008
- Large Scale Sequencing Colloquium participant - 2008
reviewer or editor for
event host
Background
education and training
- Ph.D. in Environmental Microbiology, University of Colorado 2001
- B.A. in Integrative Biology, University of California 1992
awards and honors
- NIH Director's New Innovator Award, 2010
- Beckman Young Investigator, 2009
- Hartwell Investigator, 2009
- Kavli Fellow, 2007
- Ruth L. Kirschstein National Research Service Award, 2004
- Research Associateship, 2001
- Doctoral Dissertation Improvement Grant, 2001
- Student Travel Grant, 2001
- Dept of Ecology and Evolutionary Biology Research Grant, 2000
- Beverly Sills Research Grant Award, 1998
- Biosphere-Atmosphere Research Training Fellowship, 1996
- Packard Fellow
Other
college
- CALS
research keyword
- host-microbial interactions
- human microbiome
- microbiology
name prefix
- Dr.