Publications

2020
Mineeva, O.; Rojas-Carulla, M.; Ley, R. E.; Schoelkopf, B.; and Youngblut, N. D.: 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, 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. mBio, 11 (1) e03235-19. doi: https://doi.org/10.1128/mBio.03235-19. (2020)

Clasen, S. J. and Ley, R. E.: Iron deficiency causes wrinkles in host-commensal relationships. Cell Metabolism 31, 8-10. doi: https://doi.org/10.1016/j.cmet.2019.12.003. (2020).

2019

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: https://doi.org/10.1038/s41467-019-13538-y. (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: https://doi.org/10.1093/bioinformatics/btz899. (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: https://doi.org/10.1128/mSystems.00612-19. (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: https://doi.org/10.1186/s12915-019-0699-4. (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: https://doi.org/10.1186/s13059-019-1804-2. (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: https://doi.org/10.1038/s41467-019-10191-3. (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: https://doi.org/10.1128/mSystems.00261-19. (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: https://doi.org/10.1016/j.chom.2019.03.001. (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: https://doi.org/10.1016/j.chom.2019.01.019. (2019).

2018

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: https://doi.org/10.1128/mSystems.00031-18. (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: https://doi.org/10.1093/cdn/nzy070. (2018).

Walters, W. A.; Jin, Z.; Youngblut, N.; Wallace, J. G.; Sutter, J.; Zhang, W.; González-Peña, A.; Peiffer, J.; Koren,  O.; Shi,  Q.; Knight, R.; Glavina del Rio, T.; Tringe, S. G.; Buckler, E. S.; Dangl, J. L. and Ley, R. E.: Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci USA 115: 7368-7373. doi: https://doi.org/0.1073/pnas.1800918115. (2018).

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).

2017

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). 

2016

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 Parsonnet, J.: 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). 

2015

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 Ley, R. E.: 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 Qi L.: 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).

2014

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.

2013

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).

2012

Koren, O.; Goodrich, J. K.; Cullender, T. C.; Spor, A.; Laitinen, K.; Backhed, H.; Gonzalez, A.; Werner, J. J.; Angenent, L. T.; Knight, R.; Bäckhed, 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 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, 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).

2011

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 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, 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.: 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).

2010

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).

2009

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).

2008

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 http://www.genome.gov/10002154. (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.; Zou, X. 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).

BioRxiv

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).