Publications
_{Microbiome Science}

Tran, H.; Ley, R.; Gewirtz, A.; Chassaing, B.: Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nature Communications 10, 5650 (2019)

Hayward, R.; Marsh, J.; Humphrys, M.; Huston, W.; Myers, G.: Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution. Frontiers in Cellular and Infection Microbiology 9, 392 (2019)

Janzon, A.; Goodrich, J.; Koren, O.; TEDDY Study Group; Waters, J.; Ley, R.: Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems 4 (6), e00612-19 (2019)

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

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.: Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37 (9), p. 1091 (2019)

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

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)

Barnett, S.; Youngblut, N.; Buckley, D.: Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP. In: Methods in Molecular Biology. Springer, US (2019)

Marsh, J.; Hayward, R.; Shetty, A.; Mahurkar, A.; Humphrys, M.; Myers, G.: Dual RNA-Seq of Chlamydia and Host Cells. In: Methods in Molecular Biology, Vol. 2042. Springer, US (2019)

Schmidt, V.; Ley, R.: The African Microbiome: Clues of human adaptation and population history. In: Modern human origins and dispersal, pp. 239 - 260 (Eds. Sahle, Y.; Reyes-Centeno, H.; Bentz, C.). Kerns, Tübingen, Germany (2019)

Ley, R.: Microbiota and metabolic diseases. EMBO FEBS Lecture Course: The new microbiology, Spetses Island, Greece (2019)

Ley, R.: Coevolution of humans with their microbiomes. EMBO FEBS Lecture Course: The new microbiology, Spetses Island, Greece (2019)

Sutter, J.; Youngblut, N.; Walters, W.; Ley, R.: Comparative metagenomic analysis of highly abundant Pseudomonas within the maize rhizosphere. XVIII Congress of the International Society for Molecular Plant-Microbe Interactions (IS-MPMI 2019), Glasgow, UK (2019)

de la Cuesta-Zuluaga, J.; Ley, R.; Youngblut, N.: Struo: a pipeline for building custom databases for common metagenome profilers. German Conference on Bioinformatics (GCB 2019), Heidelberg, Germany (2019)

Heaver, S.; Ley, R.: A transcriptomic approach to identify the sphingolipid metabolic pathway in gut-associated Bacteroides. 13th Sphingolipid Club & 10th International Ceramide Conference, Cascais, Portugal (2019)