Publications

2020

Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS and Ley RE. Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels. Nature Communications 11:2471 (2020)

Mineeva O, Rojas-Carulla M, Ley RE, Schoelkopf B and Youngblut ND. DeepMAsED: Evaluating the quality of metagenomics assemblies. Bioinformatics btaa124. doi: 10.1093/bioinformatics/btaa124 (2020)

Ruaud A, Esquivel-Elizondo S, de la Cuesta-Zuluaga J, Waters JL, Angenent LT, Youngblut ND and Ley RE. Syntrophy via Interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut. mBio 11 (1) e03235-19 (2020)

Clasen SJ and Ley RE. Iron deficiency causes wrinkles in host-commensal relationships. Cell Metabolism 31, 8-10 (2020)

2019

Tran HQ, Ley RE, Gewirtz AT and Chassaing B. Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nature Communications 10, 5650 (2019) 

de la Cuesta-Zuluaga J, Ley RE and Youngblut ND. Struo: a pipeline for building custom databases for common metagenome profilers. Bioinformatics (2019)

Janzon A, Goodrich JK, Koren O, TEDDY Study Group, Waters JL, Ley RE. Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems 4(6) (2019)

Waters JL and Ley RE. The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biology 17: 83 (2019)

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

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley RE, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Ro beson II MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R and Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37:52–857 (2019)

Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE and Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications 10: 2200 (2019) 

de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R and Thackray VG. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 4:e00261-19 (2019)

Schmidt VT and Ley RE. 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 AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG and Ley RE. Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host & Microbe 25: 553-564 (2019)

Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector T, Bell JT, Youngblut ND, Hewson I, Reyes A and Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. (2019). Cell Host & Microbe 25: 261-272 (2019)

2018

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzales A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jaclson MA, Jannsen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko C, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E and Zhu Q. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18 (2018)

Alves da Silva AV, Oliveira SB, Di Rienzi SC, Dehan LM, Rood JK, Carreira VS, Le H, Maier EA, Betz KJ, Aihara E, Ley RE, Preidis GE, Shen L  and Moore SR. Murine methyl donor deficiency impairs early growth in association with dysmorphic small intestinal crypts and reduced gut microbial diversity. Current Developments in Nutrition 3:nzy070 (2018)

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi  Q, Knight R, Glavina del Rio T, Tringe SG, Buckler ES, Dangl JL and Ley RE. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences of the United States of America 115: 7368-7373 (2018)

Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J and Ley RE. Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. eLife 7:e32581. (2018).

Heaver SL, Johnson EL and Ley RE. Sphingolipids in host-microbial interactions. Current Opinion in Microbiology 43: 92-99 (2018)

Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hatori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Othman H, O'Toole PW, Quince C, Reman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R and Bork P. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology  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 DS, Lu TY, Lebens S, Jin Z, McDonald M, Klein AP, Fletcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Bringe SG, Wolke T and Dang JL. Genomic features of bacterial adaptation to plants. Nature Genetics 50: 138-150 (2018)

2017

Goodrich JK, Davenport ER, Clark AG and Ley RE. The relationship between the human genome and microbiome comes into view. Annual Review of Genetics 51: 413-433 (2017)

Guss JD, Horsfield MW, Fontenele FF, Sandoval TN, Luna M, Apoorva F, Lima SF, Bicalho RC, Singh A, Ley RE, van der Meulen MC, Goldring SR and Hernandez CJ. Alterations to the gut microbiome impair bone strength and tissue material properties. Journal of Bone and Mineral Research 32: 1343-1353 (2017)

McGavigan AK, Henseler ZM, Garibay D, Butler SD, Jayasinghe S, Ley RE, Davisson RL and Cummings BP. Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice. Disease Models & Mechanisms 10: 235-243 (2017)

Johnson EL, Heaver SL, Walters WA and Ley RE. Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. Journal of Molecular Medicine (Berl) 95: 1-8 (2017) 

2016

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

Davenport ER, Goodrich JK, Bell JT, Spector TD, Ley RE and Clark AG. ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics 17: 941 (2016)

Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD and Bell JT. Heritbale components of the human fecal microbiome are associated with visceral fat. Genome Biology 17: 189 (2016)

Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE and Hanson MR. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 4: 30 (2016)

Poole AC, Pischel L, Ley C, Suh G, Goodrich JK, Taggerty TD, Ley RE and Parsonnet J. Crossover control study of the effect of personal care products containing Triclosan on the microbiome. mSphere 1: e00056-15 (2016)

Ley RE and Gewirtz AT. Corralling flagellated microbiota. The New England Journal of Medicine 375: 85-87 (2016)

Goodrich JK, Davenport ER, Waters JL, Clark AG and Ley RE. Cross-species comparisons of host genetic associations with the microbiome. Science 352: 532-535 (2016)

Goodrich JK, Davenport ER, Jackson MA, Beaumont M, Knight R, Spector TD, Bell JT, Clark AG and Ley RE. Genetic determinants of the gut microbiome assessed in UK Twins. Cell Host & Microbe 19: 731-43 (2016)

Jackson M, Jeffrey IB, Beaumont M, Bell JT, Clark AG, Ley RE, O’Toole PW, Spector TD and Steves CJ. Signatures of frailty in the gut microbiota. Genome Medicine 29: 8 (2016)

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

Jackson MA, Goodrich JK, Maxan ME, Fredberg DE, Abrams JA, Poole AC, Sutter JL, Welter D, Ley RE, Bell JT, Spector TD and Steves CJ. Proton pump inhibitors alter the composition of the gut microbiota. Gut 65: 749-756 (2016) 

2015

Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley RE, Walter MT and Angenent LT. Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics. Frontiers in Microbiology 6: 1523 (2015)

Jin Z, Di Renzi SC, Janzon A, Werner JJ, Angenent LT, Fowler DM, Dangl JL and Ley RE. Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. Applied and Environmental Microbiology  82: 1050-1059 (2015)

Sun S, Lourie R, Cohen SB, Ji Y, Goodrich JK, Poole AC, Ley RE, Denkers EY, McGuckin MA, Long Q, Duhamel GE, Simpson KW and Qi L. Epithelial Sel1L is required for the maintenance of intestinal homeostasis. Molecular Biology of the Cell 27: 483-490 (2015)

McGavigan AK, Garibay D, Henseler ZM, Chen J, Bettaieb A, Haj FG, Ley RE, Chouinard ML and Cummings BP. TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice. Gut 66: 226-234 (2015)

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D and Clark AG. Host genetic variation impacts microbiome composition across body sites. Genome Biology 16: 191 (2015)

Barrios C, Beaumont  M, Palmister T, Villar J, Goodrich JK, Clark A, Pascual J, Ley RE, Spector TD, Bell JT 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 RE and Gewirtz AT. 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 AC, Dangl JL, Knight R, Ley RE and Schulze-Lefert P. Microbiota and host nutrition across plant and animal kingdoms. Cell Host & Microbe 17: 603-616 (2015)

Ley RE. The Gene-Microbe Link. Nature 518: S7 (2015)

Panke-Buisse K, Poole AC, Goodrich JK, Ley RE and Kao-Kniffin J. Selection on plant microbiomes reveals reproducible impacts on plant function. ISME Journal 9: 980-989 (2015)

2014

Kumar H, Lund R, Laiho A, Lundelin K, Ley RE, 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 JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG and Ley RE. Human genetics shape the gut microbiome. Cell 159: 789-799 (2014)

Chassaign B, Ley RE and Gewirtz AT. 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 JK, Kim H, Poole AC, Duhamel GE, Ley RE 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 RE, 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 CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Marhurkar A and Ravel J. Scientists for Advancement of Microbiome Research, O. White. Advancing the Microbiome Research Community. Cell 159: 227-230 (2014)

Goodrich JK, Di Renzi SC, Poole AC, Koren O, Walters WA, Caporaso G, Knight R and Ley RE. Conducting a Microbiome Study. Cell 17: 250-262 (2014)

Leifer CA, McConkey C, Li S, Chassaing B, Gewirtz AT and Ley RE. Linking genetic variation in Toll-like Receptor 5 genes to the gut microbiome’s potential to cause inflammation. Immunology Letters 162: 3-9 (2014)

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

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

2013

Cullender TC, Chassaing B, Janzon A, Kumar K, Muller C, Werner JJ, Angenent LT, Bell ME, Hay AG, Peterson DA, Walter J, Vijay-Kumar M, Gewirtz AT and Ley RE. Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host & Microbe 14: 571-581 (2013)

Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF and Ley RE.  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 SG, Dangl JL, Buckler ES and Ley RE. Diversity and heritability of the Maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences of the United States of America 110: 6548-6553 (2013)

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

Petschow B, Doré J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G, Hutton J, Klaenhammer TR, Ley RE, Nieuwdorp M, Pot B, Relman D, Serafijn A, Sanders ME. Probiotics, prebiotics, and the host microbiome: the science of translation. Annals of the New York Academy of Sciences 1306: 1-17 (2013)

Peiffer JA and Ley RE. Exploring the maize rhizosphere microbiome in the field: A glimpse into a highly complex system. Communicative & Integrative Biology 6: e25177 (2013)

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

2012

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

Carvalho FA, Koren O, Johansson M, Nalbantoglu I, Aitken JD, Su Y, Walters WA, González Peña A, Clemente JC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE and Gewirtz AT. Transient inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host & Microbe 12: 139-152 (2012) 

Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrekston A, Kunin V, del Rio TG, Edgar R, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG and Dangl JL. Defining the core Arabidopsis thaliana root microbiome. Nature 486: 207-214 (2012) 

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

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

Brook SM, van Coeverden de Groot P, Scott C, Boag P, Long B, Ley RE, Reischer GH, Williams AC, Mahood SP, 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 YS, Koren O, Fricker A, Nookaew I, Nielsen J, Ley RE 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 JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R and Ley RE. Impact of training sets on classification of high-throughput bacterial 16S rRNA Gene Surveys. The ISME Journal 6: 94-103 (2012)

Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M and Gewirtz AT. 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 RE, Leibel RL. Responses of gut microbiota to weight loss in obese and lean mice. Obesity 20: 738-747 (2012)

2011

Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley RE, Wakeland EK and Hooper LV.  The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334: 255-258 (2011)

Ran-Ressler RR, Khailova L, Arganbright KM, Adkins-Rieck CK, Jouni ZE, Koren O, Ley RE, Brenna JT 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 CB, Knight R, Fagerberg B, Ley RE and Bäckhed 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 RE, Field D, Knight R, DeSantis TZ and Kelley ST. Supervised classification of microbiota mitigates mislabeling errors. The ISME Journal 5: 570-573 (2011)

Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT and Ley RE. 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 RE and Gordon JI. The human intestinal microbiota and microbiome. Textbook of Gastroenterology, Fifth edition (Dr. Tadataka Yamada, Ed.). Blackwell Publishing (2011)

Dominguez-Bello MG, Blaser MJ, Ley RE 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 RE.  Unraveling the effects of environment and host genotype on the gut microbiome. Nature Reviews Microbiology 9:279-90 (2011)

2010

Caporaso JG, Kaczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello E, Fierer N, Gonzales Pena A, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone C, McDonald D, Muegge B, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, van Treuren W, Walters WA, 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 JD, Carvalho FA, Mwangi S, Srinivasa S, Sitaraman SV, Cullender T, Knight R, Ley RE and Gewirtz AT. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328: 228-231 (2010)

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

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

2009

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R and Gordon JI. A core gut microbiome in obese and lean twins. Nature 457: 480-484 (2009)

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

2008

Ley RE, Lozupone CA, Hamady M, Knight R and Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota (Analysis). Nature Reviews Microbiology 6: 776-788 (2008)

Wen L, Volchkov P, Ley RE, Stranges P, Avanesyan L, Stonebraker A, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI and Chervonsky AV. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455:1109-1113 (2008)

Godoy-Vitorino F, Ley RE, Gao Z, Pei Z, Ortiz-Zuazaga H, Pericchi LR, Garcia-Amado MA, Michelangeli F, Blaser MJ, Gordon JI and Dominguez-Bello MG. The crop bacterial community of the hoatzin, a neotropical folivorous flying bird. Applied and Environmental Microbiology 74: 5905-5912 (2008)

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R and Gordon JI. Evolution of mammals and their gut microbes. Science 320: 1647-1651 (2008)

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

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett C, Knight R and Gordon JI. The human microbiome project. Nature 449: 804-810 (2007)

Ley RE, Knight RD and Gordon JI. The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology. Environmental Microbiology 9: 3-4 (2007)

Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE and Pace NR. Eucaryotic Diversity in a Hypersaline Microbial Mat. Applied and Environmental Microbiology, 74: 329-332 (2008)

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD and Gordon JI. Evolution of symbiotic bacteria in the distal human intestine.  PLoS Biology 5: e156 (2007)

Turnbaugh PJ, Ley  RE, Mahowald M, Magrini V, Mardis ER and Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031 (2006)

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

Rawls JF, Mahowald MM, Ley RE and Gordon JI. 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 FR, Ley RE, Sonnenburg JL and Gordon JI. The human intestinal microbiota and its relationship to energy balance. Scandinavian Journal of Food and Nutrition 50: 121-123 (2006)

Ley RE, Peterson DA and Gordon JI. 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 RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin M and Pace NR. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 72: 3685-3695 (2006)

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

Bäckhed FR, Ley RE, Sonnenburg JL, Peterson DA and Gordon JI. Host-bacterial mutualism in the human intestine. Science 307: 1915-1920 (2005)

Gordon JI, Ley RE, Wilson R, Mardis E, Xu J, Fraser CM and Relman DA. Extending our view of self: the human gut microbiome initiative (HGMI). NHGRI White paper (prioritized), published online at http://www.genome.gov/10002154 (2005)

Ley RE, Williams MW and Schmidt SK. 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 SK, Lipson DA, Ley RE, Fisk MC and West AE. The impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils. Biogeochemistry 69: 1-17 (2004)

Cleveland CC, Townsend AR, Constance BC, Ley RE and Schmidt SK. Soil microbial dynamics in Costa Rica:  seasonal and biogeochemical constraints. Biotropica 36: 184-195 (2004)

Jakosky BM, Nealson KH, Bakermans C, Ley RE and Mellon MT. Sub-freezing activity of microorganisms and the potential habitability of Mars’ polar regions. Astrobiology 3: 343-351 (2003)

Spear JS, Ley RE, Berger AB and Pace NR. The complexity of the genome pool in natural microbial ecosystems:  The Guerrero Negro experience. Biological Bulletin 204: 168-173 (2003)

Ley RE and Schmidt SK. 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 MA, D'Antonio CM and Ley RE. 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 RE, Schmidt SK, Zou X and Seastedt TR. Soil ecological interactions: comparisons between tropical and subalpine forests. Oecologia 128: 549-556 (2001)

Ley RE, Lipson DA and Schmidt SK. Microbial biomass levels in high elevation vegetated and barren talus soils. Soil Science Society of America Journal 65: 111-117 (2001)

Schmidt SK and Ley RE. 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 RE and D’Antonio CM. Alien plant invasions decrease potential rates of nitrogen fixation in dry tropical forests of Hawai’i.  Oecologia 113: 179-18 (1998)

D'Antonio CM, Tunison JT, Ley RE and Loh R. Ongoing research into revegetation of degraded dry forest in Hawai’i. Restoration and Management Notes, Winter (1994)

BioRxiv

Schmidt V, Enav H, Spector T, Youngblut ND,  and R Ley. Strain-level analysis of Bifidobacterium spp. from gut microbiomes of adults of differing lactase persistence genotypes. bioRxiv 2020.07.16.207811 https://www.biorxiv.org/content/10.1101/2020.07.16.207811v1 (2020)

Youngblut ND, de la Cuesta-Zuluaga and RE Ley. Incorporating genome-based phylogeny and trait similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. bioRxiv 2020.07.16.207845 https://www.biorxiv.org/content/10.1101/2020.07.16.207845v1 (2020)

Youngblut ND, de la Cuesta-Zuluaga J, Reischer GH, Dauser S,  Schuster N, Walzer C, Stalder G, Farnleitner A, and RE Ley. Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity. bioRxiv 135962. doi: https://www.biorxiv.org/content/10.1101/2020.06.05.135962v1 (2020)

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: https://doi.org/10.1101/872333. (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: https://doi.org/10.1101/774372. (2019).

Rojas-Carulla M., Ley R. E., Schoelkopf B., and Youngblut N. D.: DeepMAsED: Evaluating the Quality of Metagenomic Assemblies. bioRxiv. doi: https://doi.org/10.1101/763813. (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: https://doi.org/10.1101/722744 (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: https://doi.org/10.1101/637959. (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: https://doi.org/10.1101/484006(2018).

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: https://doi.org/10.1101/632877. (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: https://doi.org/10.1101/359737. (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: https://doi.org/10.1101/509273. (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: https://doi.org/10.1101/537894. (2019).

Rojas-Carulla M., Tolstikhin I., Luque G., Youngblut N., Ley R. and Schölkopf B.: GeNet: Deep Representations for Metagenomics. arXiv https://arxiv.org/pdf/1901.11015.pdf. (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: https://doi.org/10.7287/peerj.preprints.27295v2. (2018).