Antibiotics, Pediatric Dysbiosis, and Disease von Vangay, Pajau, Ward, Tonya, Gerber, Jeffrey S., Knights, Dan

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Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome von Knights, Dan, Lassen, Kara G, Xavier, Ramnik J

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UniFrac: an effective distance metric for microbial community comparison von Lozupone, Catherine, Lladser, Manuel E, Knights, Dan, Stombaugh, Jesse, Knight, Rob

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Supervised classification of human microbiota von Knights, Dan, Costello, Elizabeth K, Knight, Rob

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Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies von Gohl, Daryl M, Vangay, Pajau, Garbe, John, MacLean, Allison, Hauge, Adam, Becker, Aaron, Gould, Trevor J, Clayton, Jonathan B, Johnson, Timothy J, Hunter, Ryan, Knights, Dan, Beckman, Kenneth B

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Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans von Johnson, Abigail J., Vangay, Pajau, Al-Ghalith, Gabriel A., Hillmann, Benjamin M., Ward, Tonya L., Shields-Cutler, Robin R., Kim, Austin D., Shmagel, Anna Konstantinovna, Syed, Arzang N., Walter, Jens, Menon, Ravi, Koecher, Katie, Knights, Dan

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Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans von Muegge, Brian D., Kuczynski, Justin, Kinghts, Dan, Clemente, Jose C., González, Antonio, Fontana, Luigi, Henrissat, Bernard, Knight, Rob, Gordon, Jeffrey I.

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences von Langille, Morgan G I, Zaneveld, Jesse, Caporaso, J Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A, Clemente, Jose C, Burkepile, Deron E, Vega Thurber, Rebecca L, Knight, Rob, Beiko, Robert G, Huttenhower, Curtis

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Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome von Maldonado-Gómez, María X., Martínez, Inés, Bottacini, Francesca, O’Callaghan, Amy, Ventura, Marco, van Sinderen, Douwe, Hillmann, Benjamin, Vangay, Pajau, Knights, Dan, Hutkins, Robert W., Walter, Jens

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Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome von Mars, Ruben A.T., Yang, Yi, Ward, Tonya, Houtti, Mo, Priya, Sambhawa, Lekatz, Heather R., Tang, Xiaojia, Sun, Zhifu, Kalari, Krishna R., Korem, Tal, Bhattarai, Yogesh, Zheng, Tenghao, Bar, Noam, Frost, Gary, Johnson, Abigail J., van Treuren, Will, Han, Shuo, Ordog, Tamas, Grover, Madhusudan, Sonnenburg, Justin, D’Amato, Mauro, Camilleri, Michael, Elinav, Eran, Segal, Eran, Blekhman, Ran, Farrugia, Gianrico, Swann, Jonathan R., Knights, Dan, Kashyap, Purna C.

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Captivity humanizes the primate microbiome von Clayton, Jonathan B., Vangay, Pajau, Huang, Hu, Ward, Tonya, Hillmann, Benjamin M., Al-Ghalith, Gabriel A., Travis, Dominic A., Long, Ha Thang, Van Tuan, Bui, Van Minh, Vo, Cabana, Francis, Nadler, Tilo, Toddes, Barbara, Murphy, Tami, Glander, Kenneth E., Johnson, Timothy J., Knights, Dan

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Functional Genomics of Host–Microbiome Interactions in Humans von Luca, Francesca, Kupfer, Sonia S., Knights, Dan, Khoruts, Alexander, Blekhman, Ran

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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea von Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G., Belda-Ferre, Pedro, Al-Ghalith, Gabriel A., Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B., Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z., Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T., Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, Knight, Rob

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Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor von Smith, Michelle I., Yatsunenko, Tanya, Manary, Mark J., Trehan, Indi, Mkakosya, Rajhab, Cheng, Jiye, Kau, Andrew L., Rich, Stephen S., Concannon, Patrick, Mychaleckyj, Josyf C., Liu, Jie, Houpt, Eric, Li, Jia V., Holmes, Elaine, Nicholson, Jeremy, Knights, Dan, Ursell, Luke K., Knight, Rob, Gordon, Jeffrey I.

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A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets von Koren, Omry, Knights, Dan, Gonzalez, Antonio, Waldron, Levi, Segata, Nicola, Knight, Rob, Huttenhower, Curtis, Ley, Ruth E

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Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults von Vanegas, Sally M, Meydani, Mohsen, Barnett, Junaidah B, Goldin, Barry, Kane, Anne, Rasmussen, Helen, Brown, Carrie, Vangay, Pajau, Knights, Dan, Jonnalagadda, Satya, Koecher, Katie, Karl, J Philip, Thomas, Michael, Dolnikowski, Gregory, Li, Lijun, Saltzman, Edward, Wu, Dayong, Meydani, Simin Nikbin

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Evaluating the Information Content of Shallow Shotgun Metagenomics von Hillmann, Benjamin, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Zhu, Qiyun, Gohl, Daryl M, Beckman, Kenneth B, Knight, Rob, Knights, Dan

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Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment von Burns, Michael B, Lynch, Joshua, Starr, Timothy K, Knights, Dan, Blekhman, Ran

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Cohabiting family members share microbiota with one another and with their dogs von Song, Se Jin, Lauber, Christian, Costello, Elizabeth K, Lozupone, Catherine A, Humphrey, Gregory, Berg-Lyons, Donna, Caporaso, J Gregory, Knights, Dan, Clemente, Jose C, Nakielny, Sara, Gordon, Jeffrey I, Fierer, Noah, Knight, Rob

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Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat von Kirk Harris, J, Gregory Caporaso, J, Walker, Jeffrey J, Spear, John R, Gold, Nicholas J, Robertson, Charles E, Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob, Pace, Norman R

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