Ruaud, A., Esquivel-Elizondo, S., de la Cuesta-Zuluaga, J., Waters, J. L., Angenent, L. T., Youngblut, N. D. and Ley R. E.: Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio, 11 (1) e03235-19. doi: (2020)

Clasen, S. J. and Ley, R. E.: Iron Deficiency Causes Wrinkles in Host-Commensal Relationships. Cell Metab 31, 8-10. doi: (2020).


Tran, H. Q., Ley, R. E. and Gewirtz, A.T. et al.: Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nat Commun 105650. doi: (2019). 

de la Cuesta-Zuluaga, J., Ley, R. E. and Youngblut, N. D.: Struo: a pipeline for building custom databases for common metagenome profilers. Bioinformatics. doi: (2019).

Janzon A., Goodrich J.K., Koren O., TEDDY Study Group, Waters J.L., Ley R.E.: Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut, mSystems, 4(6). doi: (2019).

Waters J. L. and Ley R. E.: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biol 17: 83. doi: (2019).

Knight R., Ley R. E., Raes J. and Grice E. A.: Expanding the scope and scale of microbiome research. Genome Biology 20: 191. doi: (2019).

Bolyen E., Rideout J. R., Dillon M. R., Bokulich N. A., Abnet C., Al-Ghalith G. A., Alexander H., Alm E. J., Arumugam M., Asnicar F., Bai Y., et al.: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37:52–857. (2019).

Youngblut N. D., Reischer G. H., Walters W., Schuster N., Walzer C., Stalder G., Ley R. E. and Farnleitner A. H.: Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun 10: 2200. doi: (2019). 

de la Cuesta-Zuluaga J., Kelley S. T., Chen Y., Escobar J. S., Mueller N. T., Ley R. E., McDonald D., Huang S., Swafford A. D., Knight R. and Thackray V. G.: Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 4:e00261-19. doi: (2019).

Schmidt V. T. and Ley R. E.: The African Microbiome: Clues of human adaptation and population history. In Sahle Y., Reyes-Centeno H., and Bentz C. (Eds.), Modern Human Origins and Dispersal. Kems Verlag, Tübingen, Germany. (2019). 

Poole A. C., Goodrich J. K., Youngblut N. D., Luque G. G., Ruaud A., Sutter J. L., Waters J. L., Shi Q., El-Hadidi M., Johnson L. M., Bar H. Y., Huson D. H., Booth J. G. and Ley R. E.: Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host & Microbe 25: 553-564. doi: (2019).

Moreno-Gallego J. L., Chou S. P., Di Rienzi S. C., Goodrich J. K., Spector T., Bell J. T., Youngblut N., Hewson I., Reyes A. and Ley R. E.: Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. (2019). Cell Host & Microbe 25: 261-272. doi: (2019).


McDonald D., Hyde E., Debelius J. W., Morton J. T., Gonzales A., et al.: American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. doi: (2018).

Alves da Silva A. V., Oliveira S. B., Di Rienzi S. C., Dehan L. M., Rood J. K., Carreira V. S., Le H., Maier E. A., Betz K. J., Aihara E., Ley R. E., Preidis G.E., Shen L.  and Moore S. R.: Murine methyl donor deficiency impairs early growth in association with dysmorphic small intestinal crypts and reduced gut microbial diversity. Current Dev Nutr. 3:nzy070. doi: (2018).

Walters W. A., Jin Z., Youngblut N., Wallace J. G., Sutter J., Zhang W., González-Peña A., Peiffer J., Koren  O., Shi  Q., Rob Knight, Glavina del Rio T., Tringe S. G., Buckler E. S., Dangl J. L., and R. E. Ley. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci USA 115: 7368-7373. doi:

Di Rienzi S. C., Jacobson J., Kennedy E. A., Bell M. E., Shi Q., Waters J. L., Lawrence P., Brenna J. T., Britton R. A., Walter J., and Ley R. E.:  Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. eLife 7:e32581 (2018).

Heaver S. L., Johnson E. L. and Ley R. E.: Sphingolipids in host-microbial interactions. Curr Opin Microbiol. 43: 92-99 (2018).

Costea P. I., Hildebrand F., Manimozhiyan A., Bäckhed F., Blaser M. J., Bushman F. D., de Vos W. M., Ehrlich S. D., Fraser C. M., Hatori M., Huttenhower C., Jeffery I. B., Knights D., Lewis J. D., Ley R. E., Othman H., O'Toole P. W., Quince C., Reman D. A., Shanahan F., Sunagawa S., Wang J., Weinstock G. M., Wu G. D., Zeller G., Zhao L., Raes J., Knight R. and Bork P.: Enterotypes in the landscape of gut microbial community composition. Nat Microbiol.  3: 8-16 (2018).

Levy A., Salas Gonzalez I., Mittelviefhaus M., Clingenpeel S., Herrera Paredes S., Miao J., Wang K., Devescoyvi G., Stillman K., Monteiro F., Rangel Alvarez B., Lundberg D. S., Lu T. Y., Lebens S., Jin Z., McDonald M., Klein A. P., Fletcher M. E., Rio T. G., Grant S. R., Doty S. L., Ley R. E., Zhao B., Venturi V., Pelletier D. A., Vorholt J. A., Bringe S. G., Wolke T. and Dang J. L.: Genomic features of bacterial adaptation to plants. Nat Genet. 50: 138-150 (2018).


Goodrich J. K., Davenport E. R., Clark A. G. and Ley R. E.: The relationship between the human genome and microbiome comes into view. Annu Rev Genet. 51: 413-433. (2017).

Guss J. D., Horsfield M. W., Fontenele F. F., Sandoval T. N., Luna M., Apoorva F., Lima S. F., Bicalho R. C., Singh A., Ley R. E., van der Meulen M. C., Goldring S. R. and Hernandez C. J.: Alterations to the gut microbiome impair bone strength and tissue material properties. J. Bone Miner Res. 32: 1343-1353. (2017).

McGavigan A. K., Henseler Z. M., Garibay D., Butler S. D., Jayasinghe S., Ley R. E., Davisson R. L. and Cummings B. P.: Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice. Dis Model Mech. 10: 235-243. (2017).

Johnson E. L., Heaver S. L., Walters W. A. and Ley R. E.: Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. J Mol Med. (Berl) 95: 1-8. (2017). 


Women in Metabolism: Part IV. Cell Metabolism Voices. 24: 767-770. (2016).

Davenport E. R., Goodrich J. K., Bell J. T., Spector T. D., Ley R. E. and Clark A. G.: ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics 17: 941. (2016).

Beaumont M., Goodrich J. K., Jackson M. A., Yet I., Davenport E. R., Vieira-Silva S., Debelius J., Pallister T., Mangino M., Raes J., Knight R., Clark A. G., Ley R. E., Spector T. D. and Bell J. T.: Heritbale components of the human fecal microbiome are associated with visceral fat. Genome Biol. 17: 189. (2016).

Giloteaux L., Goodrich J. K., Walters W. A., Levine S. M., Ley R. E. and Hanson M. R.: Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 4: 30. (2016).

Poole A. C., Pischel L., Ley C., Suh G., Goodrich J. K., Taggerty T. D., Ley R. E. and J. Parsonnet.: Crossover control study of the effect of personal care products containing Triclosan on the microbiome. mSphere 1: e00056-15. (2016).

Ley R. E. and Gewirtz A. T.: Corralling flagellated microbiota. N Engl J Med 375: 85-87. (2016).

Goodrich J. K., Davenport E. R., Waters J. L., Clark A. G. and Ley R. E.: Cross-species comparisons of host genetic associations with the microbiome. Science 352: 532-535. (2016).

Goodrich J. K., Davenport E. R., Jackson M. A., Beaumont M., Knight R., Spector T. D., Bell J. T., Clark A. G. and Ley R. E.: Genetic determinants of the gut microbiome assessed in UK Twins. Cell Host Microbe 19: 731-43. (2016).

Jackson M., Jeffrey I. B., Beaumont M., Bell J. T., Clark A. G., Ley R. E., O’Toole P. W., Spector T. D., and Steves C. J.: Signatures of frailty in the gut microbiota. Genome Medicine 29: 8 (2016).

Ley R. E.: Prevotella in the gut: choose carefully. Nature reviews: Gastroenterology & Hepatology (2016).

Jackson M. A., Goodrich J. K, Maxan M. E., Fredberg D. E., Abrams J. A., Poole A. C., Sutter J. L., Welter D., Ley R. E., Bell J. T., Spector T. D. and Steves C. J.: Proton pump inhibitors alter the composition of the gut microbiota. Gut 65: 749-756. (2016). 


Friedman E. S., McPhillips L. E., Werner J. J., Poole A. C., Ley R. E., Walter M. T. and Angenent L. T.: Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics. Front. Microbiol. 6: 1523. (2015). 

Jin Z., Di Renzi S. C., Janzon A., Werner J. J., Angenent L. T., Fowler D. M., Dangl J. L. and R. E. Ley.  Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. Apple Environ Microbial  82: 1050-1059. (2015).

Sun S., Lourie R., Cohen S. B., Ji Y., Goodrich J. K., Poole A. C., Ley R. E., Denkers E. Y., McGuckin M. A., Long Q., Duhamel G. E., Simpson K. W. and L. Qi. Epithelial Sel1L is required for the maintenance of intestinal homeostasis. Molecular Biology of the Cell 27: 483-490 (2015).

McGavigan A.K., Garibay D., Henseler Z. M., Chen J., Bettaieb A., Haj F. G., Ley R. E., Chouinard M. L. and Cummings B. P.: TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice. Gut 66: 226-234. (2015).

Blekhman R., Goodrich J. K., Huang K., Sun Q., Bukowski R., Bell J. T., Spector T. D., Keinan A., Ley R. E., Gevers D. and Clark A. G.: Host genetic variation impacts microbiome composition across body sites. Genome Biol. 16: 191. (2015).

Barrios C., Beaumont  M., Palmister T., Villar J., Goodrich J. K, Clark A., Pascual J., Ley R. E., Spector T. D., Bell J. T. and Menni C.. Gut-microbiota-metabolite axis in early renal function decline. PloS One 10: e0134311 (2015).

Chassaing B., Koren O., Goodrich J., Poole A., Srinivasan S., Ley R. E. and Gewirtz A. T.: Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519: 92-96. (2015).

Hacquard S., Garrido-Oter R., González A., Spaepen S., Ackermann G., Lebeis S., McHardy A. C., Dangl J. L., Knight R., Ley R. E. and Schulze-Lefert P.: Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17: 603-616. (2015).

Ley, R. E.: The Gene-Microbe Link. Nature 518: S7. (2015).

Panke-Buisse K., Poole A. C., Goodrich J. K., Ley R. E. and Kao-Kniffin J.: Selection on plant microbiomes reveals reproducible impacts on plant function. ISME J 9: 980-989. (2015).


Kumar H., Lund R., Laiho A., Lundelin K., Ley R. E., Isolauri E. and Salminen S.: Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. MBio 5. pii: e02113-14. (2014).

Goodrich J. K., Waters J. L., Poole A. C., Sutter J. L., Koren O., Blekhman R., Beaumont M., Van Treuren W., Knight R., Bell J. T., Spector T. D., Clark A. G. and Ley R. E.: Human genetics shape the gut microbiome. Cell 159: 789-799. (2014).

Chassaign B., Ley R. E. and Gewirtz A. T.: Intestinal epithelial cell Toll-like Receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology S0016-5085(14)01072-5. (2014).

Ji Y., Sun S., Goodrich J. K., Kim H., Poole A. C., Duhamel G. E., Ley R. E. and Qi L.: Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Cell Reports 10: 137-149. (2014).

Perez-Munoz M., Bergstrom K., Peng V., Schmaltz R., Jimenez-Cardona R., Marsteller N., McGee S., Clavel T., Ley R. E., Xia L. and Peterson D.: Discordance between changes in the microbiota and pathogenicity in a mouse model of spontaneous colotis. Gut Microbes 5: 286-295. (2014).

Huttenhower C., Knight R., Brown C. T., Caporaso J. G., Clemente J. C., Gevers D., Franzosa E. A., Kelley S. T., Knights D., Ley R. E., Marhurkar A. and Ravel J.: Scientists for Advancement of Microbiome Research, O. White. Advancing the Microbiome Research Community. Cell 159: 227-230. (2014).

Goodrich J. K., Di Renzi S. C., Poole A. C., Koren O., Walters W. A., Caporaso G., Knight R. and Ley R. E.: Conducting a Microbiome Study. Cell 17: 250-262. (2014).

Leifer C. A., McConkey C., Li S., Chassaing B., Gewirtz A. T. and Ley R. E.: Linking genetic variation in Toll-like Receptor 5 genes to the gut microbiome’s potential to cause inflammation. Immunol Lett 162: 3-9. (2014).

Ley R. E.Clostridium difficile’s sweet tooth. Nature Medicine 4: 248-249. (2014).

Koren O. and Ley R. E.: The human intestinal microbiota and microbiome.  Textbook of Gastroenterology, Sixth edition. Blackwell Publishing, 2014.


Cullender T. C., Chassaing B., Janzon A., Kumar K., Muller C., Werner J. J., Angenent L. T., Bell M. E., Hay A. G., Peterson D. A., Walter J., Vijay-Kumar M., Gewirtz A. T. and Ley R. E.: Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe 14: 571-581. (2013).

Di Rienzi 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. and Ley R. E.:  The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2:e01102. (2013).

Peiffer J., Spor A., Jin Z., Koren O., Tringe S. G., Dangl J. L., Buckler E. S. and Ley R. E.: Diversity and heritability of the Maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110: 6548-6553. (2013).

Koren O., Knights D., Gonzalez A., Waldron L., Segata N., Knight R., Huttenhower C., Ley R. E.: A guide to Enterotypes across the human body: A meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 9: e1002863. (2013).

Petschow B., Doré J., Hibberd P., Dinan T., Reid G., Blaser M., Cani P. D., Degnan F.H., Foster J., Gibson G., Hutton J., Klaenhammer T. R., Ley R. E., Nieuwdorp M., Pot B., Relman D., Serafijn A., Sanders M. E.: Probiotics, prebiotics, and the host microbiome: the science of translation. Ann NY Acad Sci 1306: 1-17. (2013).

Peiffer J. A. and Ley R. E.: Exploring the maize rhizosphere microbiome in the field: A glimpse into a highly complex system. Commun. Integra. Bio. 6: e25177. (2013).

Ley R. E.: When guests turn hostile. Nature 494 :437-438. (2013).


Koren O., Goodrich J. K., Cullender T. C., Spor A., Laitinen K., Backhed H., Gonzalez A., Werner J. J., Angenent L. T., Knight R., Backhed F. , Isolauri E., Salminen S. and Ley R. E.: Remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 1-11. (2012).

Carvalho F. A., Koren O., Johansson M., Nalbantoglu I., Aitken J. D., Su Y., Walters W. A., González Peña A., Clemente J. C., Barnich N., Darfeuille-Michaud  A., Vijay-Kumar M., Knight R., Ley R. E. and Gewirtz A. T.: Transient inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 12: 139-152. (2012). 

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. E., Hugenholtz P., Tringe S. G. and Dangl J. L. Defining the core Arabidopsis thaliana root microbiome. Nature 486: 207-214. (2012). 

The Human Microbiome Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214. (2012).

The Human Microbiome Consortium. A framework for human microbiome research. Nature 486: 215-221. (2012). 

Brook S. M., van Coeverden de Groot P., Scott C., Boag P., Long B., Ley R. E., Reischer G. H., Williams A. C., Mahood S. P., Minh Hien T., Polet G., Cox N. and Thanh Hai B.: Integrated and novel survey methods for rhinoceros populations confirm the extinction of Rhinoceros sondaicus annamiticus from Vietnam. Biological Conservation 155: 59-67. (2012).

Larsson E., Tremaroli V., Lee Y. S., Koren O., Fricker A., Nookaew I., Nielsen J., Ley R. E. and Bäckhed F.: 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).

Werner J. J., Koren O., Hugenholtz P., DeSantis T. Z., Walters W. A., Caporaso J. G., Angenent L. T., Knight R. and Ley R. E.:  Impact of training sets on classification of high-throughput bacterial 16S rRNA Gene Surveys. The ISME Journal 6: 94-103. (2012).

Carvalho F. A., Nalbantoglu I., Ortega-Fernandez S., Aitken J. D., Su Y., Koren O., Walters W. A., Knight R., Ley R. E., Vijay-Kumar M. and Gewirtz A. T.: IL-1β promotes susceptibility of Toll-like receptor 5 KO mice to colitis. Gut: 61: 373-384. (2012).

Ravussin Y., Koren O., Spor A., LeDuc C., Gutman R., Stombaugh J., Knight R., Ley R. E., Leibel R. L.: Responses of gut microbiota to weight loss in obese and lean mice. Obesity 20: 738-747. (2012).


Vaishnava S., Yamamoto M., Severson K. M., Ruhn K. A., Yu X., Koren O., Ley R. E., Wakeland E. K. and Hooper L. V.:  The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334: 255-258. (2011).

Ran-Ressler R. R., Khailova L., Arganbright K. M., Adkins-Rieck C. K., Jouni Z. E., Koren O., Ley R. E., Brenna J. T. and Dvorak B.: Branched chain fatty acids reduce the incidence of necrotizing enterocolitis in a neonatal rat model and alter gastrointestinal microbial ecology. PLoS One 6:e29032. (2011).

Yilmaz P., the MIMARKS consortium*.  The “Minimal Information about a MARKer gene Sequence” (MIMARKS) specification.  Nature Biotechnology 29: 415-420. (2011).

Koren O., Spor A., Felin J., Fak F., Stombaugh J., Tremaroli V., Behre C. B., Knight R., Fagerberg B., Ley R. E. and Backhed F.:  Human oral, gut, and plaque microbiota in patients with atherosclerosis.  Proceedings of the National Academy of Sciences USA 108 Suppl 1: 4592-4598. (2011).

Knights D., Kuczynski J. , Koren O., Ley R. E., Field D., Knight R., DeSantis T. Z. and Kelley S. T.: Supervised classification of microbiota mitigates mislabeling errors. The ISME Journal 5: 570-573. (2011).

Koenig J. E., Spor A., Scalfone N., Fricker A. D., Stombaugh J., Knight R., Angenent L. T. and Ley R. E.: 2011. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences USA 108 Suppl1: 4578-4585. (2011).

Walter J and Ley R. E.: The human gut microbiome: ecology and recent evolutionary changes. Annual Reviews of Microbiology 65: 411-429. (2011).

Ley R. E. and Gordon J. I.: The human intestinal microbiota and microbiome.  Textbook of Gastroenterology, Fifth edition (Dr. Tadataka Yamada, Ed.). Blackwell Publishing. (2011).

Dominguez-Bello M. G., Blaser M. J., Ley R. E. and Knight R.: Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 140: 1713-1719. (2011).

Spor A., Koren O. and Ley R. E.:  Unraveling the effects of environment and host genotype on the gut microbiome.  Nature Reviews Microbiology 9:279-90. (2011).


Caporaso J. G., Kaczynski J., Stombaugh J., Bittinger K., Bushman F. D., Costello E., Fierer N., Gonzales Pena A., Goodrich J. K., Gordon J. I., Huttley G. A., Kelley S. T., Knights D., Koenig J. E., Ley R. E., Lozupone C., McDonald D., Muegge B., Pirrung M., Reeder J., Sevinsky J. R., Turnbaugh P. J., van Treuren W., Walters W. A., Widmann J., Yatsunenko T., Zaneveld J. and Knight R.: QIIME allows integration and analysis of high-throughput community sequencing data. Nature Methods 7:335-336. (2010).

Vijay-Kumar M., Aitken J. D., Carvalho F. A., Mwangi S., Srinivasa S., Sitaraman S. V., Cullender T., Knight R., Ley R. E. and Gewirtz A. T.: Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328: 228-231. (2010).

Ley R. E.:  Obesity and the human gut micro microbiome. Current Opinion in Gastroenterology 26:5-11. (2010).

Kuczynski J., Costello E. K., Nemergut D. R., Zaneveld J., Lauber C. L., Knights D., Koren O., Fierer N., Kelley S., Ley R. E., Gordon J. I. and Knight R.: Direct sequencing of the human microbiome readily reveals community differences. Genome Biology 5: 210-219 (2010).


Turnbaugh P. J., Hamady M., Yatsunenko T., Cantarel B. L., Duncan A., Ley R. E., Sogin M. L., Jones W. J., Roe B. A., Affourtit J. P., Egholm M., Henrissat B., Heath A. C., Knight R. and Gordon J. I.:  A core gut microbiome in obese and lean twins. Nature 457: 480-484. (2009).

Ley R. E.: In Person: Breaking all the rules.  Science Career Magazine, May 29 (online, 2009).


Ley R. E., Lozupone C. A., Hamady M., Knight R. and Gordon J. I.:  Worlds within worlds: evolution of the vertebrate gut microbiota (Analysis).  Nature Reviews Microbiology 6: 776-788. (2008).

Wen L., Volchkov P., Ley R. E., Stranges P., Avanesyan L., Stonebraker A., Hu C., Wong F. S., Szot G. L., Bluestone J. A., Gordon J. I. and Chervonsky A. V.:  Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455:1109-1113. (2008).

Godoy-Vitorino F., Ley R. E., Gao Z., Pei Z., Ortiz-Zuazaga H., Pericchi L. R., Garcia-Amado M. A., Michelangeli F., Blaser M. J., Gordon J. I. and Dominguez-Bello M. G.:  The crop bacterial community of the hoatzin, a neotropical folivorous flying bird. Appl Environ Microbiol 74: 5905-5912. (2008).

Ley R. E., Hamady M., Lozupone C., Turnbaugh P. J., Ramey R. R., Bircher J. S., Schlegel M. L., Tucker T. A., Schrenzel M. D., Knight R. and Gordon J. I.:  Evolution of mammals and their gut microbes. Science 320: 1647-1651. (2008).

Zaneveld J., Turnbaugh P. J., Lozupone C., Ley R. E., Hamady M., Gordon J. I., and Knight R.:  Host-bacterial coevolution and the search for new drug targets.  Current Opinion in Chemical Biology 12: 109-114. (2008).

Turnbaugh P. J., Ley R. E., Hamady M., Fraser-Liggett C., Knight R. and Gordon J. I.:  The human microbiome project. Nature 449: 804-810. (2007).

Ley R. E., Knight R. D. and Gordon J. I.:  The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.  Environmental Microbiology 9: 3-4. (2007).

Feazel L. M., Spear J. R., Berger A. B., Harris J. K., Frank D. N., Ley R. E. and Pace N. R.: Eucaryotic Diversity in a Hypersaline Microbial Mat. Appl Environ Microbiol, 74: 329-332. (2008).

Xu J., Mahowald M. A., Ley R. E., Lozupone C. A., Hamady M., Martens E. C., Henrissat B., Coutinho P. M., Minx P., Latreille P., Cordum H., Van Brunt A., Kim K., Fulton R. S., Fulton L. A., Clifton S. W., Wilson R. K., Knight R. D. and Gordon J. I.: Evolution of symbiotic bacteria in the distal human intestine.  PLoS Biology 5: e156. (2007).

Turnbaugh P. J.,Ley  R. E., Mahowald M., Magrini V. , Mardis E. R. and Gordon J. I.: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031. (2006).

Ley R. E., Turnbaugh P., Klein S. and Gordon J. I.: Human gut microbial ecology linked to obesity.  Nature 444: 1022-1023. (2006).

Rawls J. F., Mahowald M. M., Ley  R. E. and Gordon J. I.: 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).

Bäckhed F. R., Ley R. E., Sonnenburg J. L. and Gordon J. I.: The human intestinal microbiota and its relationship to energy balance.  Scandinavian Journal of Food and Nutrition 50: 121-123. (2006).

Ley R. E., Peterson D. A. and Gordon J. I.: 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).

Ley R. E., Harris J. K., Wilcox J., Spear J. R., Miller S. R., Bebout B. M., Maresca J. A., Bryant D. A., Sogin M. and Pace N. R.: Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72: 3685-3695. (2006).

Ley R. E., Bäckhed F., Turnbaugh P., Lozupone C., Knight R. and Gordon J. I.: Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences USA 31: 11070-11075. (2005).

Bäckhed F. R., Ley R. E., Sonnenburg J. L., Peterson D. A. and Gordon J. I.: Host-bacterial mutualism in the human intestine.  Science 307: 1915-1920. (2005).

Gordon J. I, Ley R. E., Wilson R., Mardis E., Xu J., Fraser C. M. and Relman D. A.: Extending our view of self: the human gut microbiome initiative (HGMI). NHGRI White paper (prioritized), published online at (2005).

Ley R. E., Williams M. W. and Schmidt S. K.: 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).

Schmidt S. K., Lipson D. A., Ley R. E., Fisk M. C. and West A. E.: The impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils. Biogeochemistry 69: 1-17. (2004).

Cleveland C. C, Townsend A. R., Constance B. C., Ley R. E. and Schmidt S. K.: Soil microbial dynamics in Costa Rica:  seasonal and biogeochemical constraints. Biotropica 36: 184-195. (2004). 

Jakosky B. M., Nealson K. H., Bakermans C., Ley R. E. and Mellon M. T.: Sub-freezing activity of microorganisms and the potential habitability of Mars’ polar regions. Astrobiology 3: 343-351. (2003).

Spear J. S., Ley R. E., Berger A. B. and Pace N. R.: The complexity of the genome pool in natural microbial ecosystems:  The Guerrero Negro experience. Biological Bulletin 204: 168-173. (2003).

Ley R. E. and Schmidt S. K.: Fungal and bacterial responses to amino acid and phenolic compound additions in high altitude barren soil. Soil Biology and Biochemistry 34: 989-995. (2002).

Mack M. A., D'Antonio C. M. and Ley R. E.: Alteration of ecosystem nitrogen dynamics by exotic plants: a case study of C4 grasses in Hawai'i. Ecological Applications 11: 1323-1335. (2002).

Gonzalez G., Ley R. E., Schmidt S. K., Xiaoming Zou and Seastedt T. R.: Soil ecological interactions: comparisons between tropical and subalpine forests. Oecologia 128: 549-556. (2001).

Ley R. E., Lipson D. A. and Schmidt S. K.: Microbial biomass levels in high elevation vegetated and barren talus soils. Soil Science Society of America Journal 65: 111-117. (2001).

Schmidt S. K. and Ley R. E.: Microbial competition and soil structure limit the expression of allelochemicals in nature.  In Allelopathy: Procedures and Processes. (S.Inderjit, Ed.).  CRC Press, p. 339-351. (1999).

Ley R. E. and D’Antonio C. M.: Alien plant invasions decrease potential rates of nitrogen fixation in dry tropical forests of Hawai’i.  Oecologia 113: 179-18. (1998).

D'Antonio C. M., Tunison J. T., Ley R. E. and Loh R.: Ongoing research into revegetation of degraded dry forest in Hawai’i. Restoration and Management Notes, Winter (1994).


Ruaud A., Esquivel-Elizondo S., de la Cuesta-Zuluaga J., Waters J. L., Angenent L. T., Youngblut N. D., and Ley R. E.: Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut. bioRxiv 872333. doi: (2019).

de la Cuesta-Zuluaga J., Ley R.E., and Youngblut N.D.: Struo: a pipeline for building custom databases for common metagenome profilers. bioRxiv 774372. doi: (2019).

Rojas-Carulla M., Ley R. E., Schoelkopf B., and Youngblut N. D.: DeepMAsED: Evaluating the Quality of Metagenomic Assemblies. bioRxiv. doi: (2019).

Schlamp F., DY Zhang, E Cosgrove, P Simecek, M Edwards, JK Goodrich, RE Ley, GA Churchill, and AG Clark. High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition. BioRxiv doi: (2019).

Janzon A., Goodrich J. K., Koren O., the TEDDY study group, Waters J. and Ley R.: Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut. BioRxiv 637959. doi: (2019).

Youngblut N. D., Reischer G. H., Walters W., Schuster N., Walzer C., Stalder G., Ley R. E. and Farnleitner A. H.: Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. BioRxiv 484006. doi:

Johnson E. L., Heaver S. L., Waters J. L., Kim B. I., Bretin A., Goodman A. L., Gewirtz A. T., Worgall T. S. and Ley R. E.: Sphingolipid production by gut Bacteroidetes regulates glucose homeostasis. BioRxiv 632877. doi: (2019).

Poole A. C., Goodrich J. K., Youngblut N. D., Luque G. G., Ruaud A., Sutter J. L., Waters J. L., Shi Q., El-Hadidi M., Johnson L. M., Bar H. Y., Huson D. H., Booth J. G. and Ley R. E.: Human salivary amylase gene copy number impacts oral and gut microbiomes. BioRxiv 359737. doi: (2019). 

Moreno-Gallego J. L., Chou S. P., Di Rienzi S. C., Goodrich J. K., Spector T., Bell J. T., Youngblut N., Hewson I., Reyes A. and Ley R. E.: Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. BioRxiv 509273. doi: (2019). 

Li S., Walters W., Chassaing B., Zhang B., Shi Q., Waters J., Gewirtz A. T., Leifer C. A. and Ley R. E.: Gut microbiota influence B cell function in a TLR5-dependent manner. BioRxiv 537894. doi: (2019).

Rojas-Carulla M., Tolstikhin I., Luque G., Youngblut N., Ley R. and Schölkopf B.: GeNet: Deep Representations for Metagenomics. arXiv (2019).

Bolyen E., Rideout J. R., Dillon M. R., Bokulich N. A., Abnet C., Al-Ghalith G. A., Alexander H., Alm E. J., Arumugam M., Asnicar F., Bai Y., et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2. doi: (2018).