Bolyen, E.; Rideout, J.; Dillon, M.; Bokulich, N.; Abnet, C.; Al-Ghalith, G.; Alexander, H.; Alm, E.; Arumugam, M.; Asnicar, F. et al.; Bai, Y.; Bisanz, J.; Bittinger, K.; Brejnrod, A.; Brislawn, C.; Brown, C.; Callahan, B.; Caraballo-Rodríguez, A.; Chase, J.; Cope, E.; Da Silva, R.; Diener, C.; Dorrestein, P.; Douglas, G.; Durall, D.; Duvallet, C.; Edwardson, C.; Ernst, M.; Estaki, M.; Fouquier, J.; Gauglitz, J.; Gibbons, S.; Gibson, D.; Gonzalez, A.; Gorlick, K.; Guo, J.; Hillmann, B.; Holmes, S.; Holste, H.; Huttenhower, C.; Huttley, G.; Janssen, S.; Jarmusch, A.; Jiang, L.; Kaehler, B.; Kang, K.; Keefe, C.; Keim, P.; Kelley, S.; Knights, D.; Koester, I.; Kosciolek, T.; Kreps, J.; Langille, M.; Lee, J.; Ley, R.; Liu, Y.-X.; Loftfield, E.; Lozupone, C.; Maher, M.; Marotz, C.; Martin, B.; McDonald, D.; McIver, L.; Melnik, A.; Metcalf, J.; Morgan, S.; Morton, J.; Naimey, A.; Navas-Molina, J.; Nothias, L.; Orchanian, S.; Pearson, T.; Peoples, S.; Petras, D.; Preuss, M.; Pruesse, E.; Rasmussen, L.; Rivers, A.; Robeson 2nd, M.; Rosenthal, P.; Segata, N.; Shaffer , M.; Shiffer , A.; Sinha, R.; Song, S.; Spear, J.; Swafford, A.; Thompson, L.; Torres, P.; Trinh, P.; Tripathi, A.; Turnbaugh, P.; Ul-Hasan, S.; van der Hooft, J.; Vargas, F.; Vázquez-Baeza, Y.; Vogtmann, E.; von Hippel, M.; Walters, W.; Wan, Y.; Wang, M.; Warren, J.; Weber, K.; Williamson, C.; Willis, A.; Xu, Z.; Zaneveld, J.; Zhang, Y.; Zhu, Q.; Knight, R.; Caporaso, J.: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37 (8), pp. 852 - 857 (2019)

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

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

Poole, A.; Goodrich, J.; Youngblut, N.; Luque, G.; Ruaud, A.; Sutter, J.; Waters, J.; Shi, Q.; El-Hadidi, M.; Johnson, L. et al.; Bar, H.; Huson, D.; Booth, J.; Ley, R.: Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host & Microbe 25 (4), pp. 553 - 564 (2019)

Moreno-Gallego, J.; Chou, S.-P.; Di Rienzi, S.; Goodrich, J.; Spector, T.; Bell, J.; Youngblut, N.; Hewson, I.; Reyes, A.; Ley, R.: Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host & Microbe 25 (2), pp. 261 - 272 (2019)

Alves da Silva, A.; de Castro Oliveira, S.; Di Rienzi, S.; Brown-Steinke, K.; Dehan, L.; Rood, J.; Carreira, V.; Le, H.; Maier, E.; Betz, K. et al.; Aihara, E.; Ley, R.; Preidis, G.; Shen, L.; Moore, S.: Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity. Current Developments in Nutrition 3 (1), nzy070 (2019)

Enav, H.; Kirzer, S.; Lindell, D.; Mandel-Gutfreund, Y.; Béjà, O.: Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nature Communications 9, 4698 (2018)

Tang, J.; Wu, Y.; Esquivel-Elizondo, S.; Sørensen, S.; Rittmann, B.: How Microbial Aggregates Protect against Nanoparticle Toxicity. Trends in Biotechnology 36 (11), pp. 1171 - 1182 (2018)

Korpela, K.; Salonen, A.; Vepsäläinen, O.; Suomalainen, M.; Kolmeder, C.; Varjosalo, M.; Miettinen, S.; Kukkonen, K.; Savilahti, W.; Kuitonen, M. et al.; de Vos, W.: Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants. Microbiome 6, 182 (2018)

Amaral-Zettler, L.; Schmidt, V.; Smith, K.: Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain. Microorganisms 6 (3), 91 (2018)

de la Cuesta-Zuluaga, J.; Corrales-Agudelo, V.; Velásquez-Mejía, E.; Carmona, J.; Arbad, J.; Escobar, J.: Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization. Scientific Reports 8, 11356 (2018)

Heaver, S.; Johnson, E.; Ley, R.: Sphingolipids in host-microbial interactions. Current Opinion in Microbiology 43, pp. 92 - 99 (2018)

Walters, W.; Jin, Z.; Youngblut, N.; Wallace, J.; Sutter, J.; Zhang, W.; González-Peña, A.; Peiffer, J.; Koren, O.; Shi, Q. et al.; Knight, R.; Glavina Del Rio, T.; Tringe, S.; Buckler, E.; Dangl, J.; Ley, R.: 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 (28), pp. 7368 - 7373 (2018)

McDonald, D.; Hyde, E.; Debelius, J.; Morton, J.; Gonzalez, A.; Ackermann, G.; Aksenov, A.; Behsaz, B.; Brennan, C.; Chen, Y. et al.; DeRight Goldasich, L.; Dorrestein, P.; Dunn, R.; Fahimipour, A.; Gaffney, J.; Gilbert, J.; Gogul, G.; Green, J.; Hugenholtz, P.; Humphrey, G.; Huttenhower, C.; Jackson, M.; Janssen, S.; Jeste, D.; Jiang, L.; Kelley, S.; Knights, D.; Kosciolek, T.; Ladau, J.; Leach, J.; Marotz, C.; Meleshko, D.; Melnik, A.; Metcalf, J.; Mohimani, H.; Montassier, E.; Navas-Molina, J.; Nguyen, T.; Peddada, S.; Pevzner, P.; Pollard, K.; Rahnavard, G.; Robbins-Pianka, A.; Sangwan, N.; Shorenstein, J.; Smarr, L.; Song, S.; Spector, T.; Swafford, A.; Thackray, V.; Thompson, L.; Tripathi, A.; Vazquez-Baeza, Y.; Vrbanac, A.; Wischmeyer, P.; Wolfe, E.; Zhu, Q.; Knight, R.; Ley, R.: American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3 (3), e00031-18 (2018)

Costea, P.; Hildebrand, F.; Arumugam, M.; Backhed, F.; Blaser, M.; Bushman, F.; de Vos, W.; Ehrlich, S.; Fraser, C.; Hattori, M. et al.; Huttenhower, C.; Jeffery, I.; Knights, D.; Lewis, J.; Ley, R.; Ochman, H.; O'Toole, P.; Quince, C.; Relman, D.; Shanahan, F.; Sunagawa, S.; Wang, J.; Weinstock, G.; Wu, G.; Zeller, G.; Zhao, L.; Raes, J.; Knight, R.; Bork, P.: Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology 3 (3), p. 388 (2018)

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

Velásquez-Mejía, E.; de la Cuesta-Zuluaga, J.; Escobar, J.: Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces. Applied Microbiology and Biotechnology 102 (1), pp. 403 - 411 (2018)

Costea, P.; Hildebrand, F.; Arumugam, M.; Backhed, F.; Blaser, M.; Bushman, F.; de Vos, W.; Ehrlich, S.; Fraser, C.; Hattori, M. et al.; Huttenhower, C.; Jeffery, I.; Knights, D.; Lewis, J.; Ley, R.; Ochman, H.; O'Toole, P.; Quince, C.; Relman, D.; Shanahan, F.; Sunagawa, S.; Wang, J.; Weinstock, G.; Wu, G.; Zeller, G.; Zhao, L.; Raes, J.; Knight, R.; Bork, P.: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology 3 (1), pp. 8 - 16 (2017)

Emmett, B.; Youngblut, N.; Buckley, D.; Drinkwater, L.: Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field. Frontiers in Microbiology 8, 2414 (2017)

Levy, A.; Salas Gonzalez, I.; Mittelviefhaus, M.; Clingenpeel, S.; Herrera Paredes, S.; Miao, J.; Wang, K.; Devescovi, G.; Stillman, K.; Monteiro, F. et al.; Rangel Alvarez, B.; Lundberg, D.; Lu, T.; Lebeis, S.; Jin, Z.; McDonald, M.; Klein, A.; Feltcher, M.; Rio, T.; Grant, S.; Doty, S.; Ley, R.; Zhao, B.; Venturi, V.; Pelletier, D.; Vorholt, J.; Tringe, S.; Woyke, T.; Dangl, J.: Genomic features of bacterial adaptation to plants. Nature Genetics 50 (1), pp. 138 - 150 (2017)