Challenges in the construction of knowledge bases for human microbiome-disease associations by Varsha Dave Badal, Dustin Wright, Yannis Katsis, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Chun-Nan Hsu

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Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides by Gajender Aleti, Jordan N. Kohn, Emily A. Troyer, Kelly Weldon, Shi Huang, Anupriya Tripathi, Pieter C. Dorrestein, Austin D. Swafford, Rob Knight, Suzi Hong

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A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities by Justin P Shaffer, Carolina S Carpenter, Cameron Martino, Rodolfo A Salido, Jeremiah J Minich, MacKenzie Bryant, Karenina Sanders, Tara Schwartz, Gregory Humphrey, Austin D Swafford, Rob Knight

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Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults by Jacobo de la Cuesta-Zuluaga, Scott T. Kelley, Yingfeng Chen, Juan S. Escobar, Noel T. Mueller, Ruth E. Ley, Daniel McDonald, Shi Huang, Austin D. Swafford, Rob Knight, Varykina G. Thackray

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Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs by Julia M. Gauglitz, James T. Morton, Anupriya Tripathi, Shalisa Hansen, Michele Gaffney, Carolina Carpenter, Kelly C. Weldon, Riya Shah, Amy Parampil, Andrea L. Fidgett, Austin D. Swafford, Rob Knight, Pieter C. Dorrestein

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High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy by Ruma Raghuvanshi, Karla Vasco, Yoshiki Vázquez-Baeza, Lingjing Jiang, James T. Morton, Danxun Li, Antonio Gonzalez, Lindsay DeRight Goldasich, Gregory Humphrey, Gail Ackermann, Austin D. Swafford, Douglas Conrad, Rob Knight, Pieter C. Dorrestein, Robert A. Quinn

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High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy by Ruma Raghuvanshi, Karla Vasco, Yoshiki Vázquez-Baeza, Lingjing Jiang, James T. Morton, Danxun Li, Antonio Gonzalez, Lindsay DeRight Goldasich, Gregory Humphrey, Gail Ackermann, Austin D. Swafford, Douglas Conrad, Rob Knight, Pieter C. Dorrestein, Robert A. Quinn

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Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment by Jeremiah J. Minich, Farhana Ali, Clarisse Marotz, Pedro Belda-Ferre, Leslie Chiang, Justin P. Shaffer, Carolina S. Carpenter, Daniel McDonald, Jack Gilbert, Sarah M. Allard, Eric E. Allen, Rob Knight, Daniel A. Sweeney, Austin D. Swafford

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu

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Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome by Bryn C. Taylor, Mohammadsobhan Sheikh Andalibi, Stephen Wandro, Kelly C. Weldon, Gregory D. Sepich-Poore, Carolina S. Carpenter, Serena Fraraccio, Donald Franklin, Jennifer E. Iudicello, Scott Letendre, Sara Gianella, Igor Grant, Ronald J. Ellis, Robert K. Heaton, Rob Knight, Austin D. Swafford

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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities by Justin P Shaffer, Clarisse Marotz, Pedro Belda-Ferre, Cameron Martino, Stephen Wandro, Mehrbod Estaki, Rodolfo A Salido, Carolina S Carpenter, Livia S Zaramela, Jeremiah J Minich, MacKenzie Bryant, Karenina Sanders, Serena Fraraccio, Gail Ackermann, Gregory Humphrey, Austin D Swafford, Sandrine Miller-Montgomery, Rob Knight

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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases by George Armstrong, Cameron Martino, Justin Morris, Behnam Khaleghi, Jaeyoung Kang, Jeff DeReus, Qiyun Zhu, Daniel Roush, Daniel McDonald, Antonio Gonazlez, Justin P. Shaffer, Carolina Carpenter, Mehrbod Estaki, Stephen Wandro, Sean Eilert, Ameen Akel, Justin Eno, Ken Curewitz, Austin D. Swafford, Niema Moshiri, Tajana Rosing, Rob Knight

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy by Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

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Correction for Zhu et al., “Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy” by Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets by Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight

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The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis PatientsSummary by Carlos G. Gonzalez, Robert H. Mills, Melissa C. Kordahi, Marvic Carrillo-Terrazas, Henry Secaira-Morocho, Christella E. Widjaja, Matthew S. Tsai, Yash Mittal, Brian A. Yee, Fernando Vargas, Kelly Weldon, Julia M. Gauglitz, Clara Delaroque, Consuelo Sauceda, Leigh-Ana Rossitto, Gail Ackermann, Gregory Humphrey, Austin D. Swafford, Corey A. Siegel, Jay C. Buckey, Jr., Laura E. Raffals, Charlotte Sadler, Peter Lindholm, Kathleen M. Fisch, Mark Valaseck, Arief Suriawinata, Gene W. Yeo, Pradipta Ghosh, John T. Chang, Hiutung Chu, Pieter Dorrestein, Qiyun Zhu, Benoit Chassaing, Rob Knight, David J. Gonzalez, Parambir S. Dulai

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American Gut: an Open Platform for Citizen Science Microbiome Research by Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight

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