Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project

by Justine W. Debelius, Yoshiki Vázquez-Baeza, Daniel McDonald, Zhenjiang Xu, Elaine Wolfe, Rob Knight
Published 2015-10-01

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

by Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
Published 2019-02-01

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiom...

by Shi Huang, Shuaiming Jiang, Dongxue Huo, Celeste Allaband, Mehrbod Estaki, Victor Cantu, Pedro Belda-Ferre, Yoshiki Vázquez-Baeza, Qiyun Zhu, Chenchen Ma, Congfa Li, Amir Zarrinpar, Yang-Yu Liu, Rob Knight, Jiachao Zhang
Published 2021-06-01

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
Published 2020-06-01

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

by Sahil Khanna, Yoshiki Vazquez-Baeza, Antonio González, Sophie Weiss, Bradley Schmidt, David A. Muñiz-Pedrogo, John F. Rainey, Patricia Kammer, Heidi Nelson, Michael Sadowsky, Alexander Khoruts, Stefan L. Farrugia, Rob Knight, Darrell S. Pardi, Purna C. Kashyap
Published 2017-05-01

Links between gut microbiome composition and fatty liver disease in a large population sample

by Matti O. Ruuskanen, Fredrik Åberg, Ville Männistö, Aki S. Havulinna, Guillaume Méric, Yang Liu, Rohit Loomba, Yoshiki Vázquez-Baeza, Anupriya Tripathi, Liisa M. Valsta, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Published 2021-01-01

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
Published 2020-02-01

Balance Trees Reveal Microbial Niche Differentiation

by James T. Morton, Jon Sanders, Robert A. Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A. Navas-Molina, Se Jin Song, Jessica L. Metcalf, Embriette R. Hyde, Manuel Lladser, Pieter C. Dorrestein, Rob Knight, Janet K. Jansson
Published 2017-01-01

From Sample to Multi-Omics Conclusions in under 48 Hours

by Robert A. Quinn, Jose A. Navas-Molina, Embriette R. Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J. Minich, Alexey V. Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J. Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C. Dorrestein, Rob Knight, Jack A. Gilbert
Published 2016-04-01

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

by Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee-Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica S. Williams-Nguyen, Michael C. Wu, Kari E. North, Justin Shaffer, Christopher C. Sollecito, Qibin Qi, Carmen R. Isasi, Tao Wang, Rob Knight, Robert D. Burk
Published 2019-11-01

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

by Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee-Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica S. Williams-Nguyen, Michael C. Wu, Kari E. North, Justin Shaffer, Christopher C. Sollecito, Qibin Qi, Carmen R. Isasi, Tao Wang, Rob Knight, Robert D. Burk
Published 2020-02-01

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

by Alexey V. Melnik, Yoshiki Vázquez-Baeza, Alexander A. Aksenov, Embriette Hyde, Andrew C. McAvoy, Mingxun Wang, Ricardo R. da Silva, Ivan Protsyuk, Jason V. Wu, Amina Bouslimani, Yan Wei Lim, Tal Luzzatto-Knaan, William Comstock, Robert A. Quinn, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S. Brouha, Nuno Bandeira, Grace Y. Lin, Forest Rohwer, Douglas J. Conrad, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein, Neha Garg
Published 2019-09-01

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

by Matthew R Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R Keefe, Jamie T Morton, Renato R M Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vázquez-Baeza, Michal Ziemski, Hazuki E Miwa, Terry A Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D Kaehler, Emily K Cope, Jessica L Metcalf, Michael S Robeson Ii, Nicholas A Bokulich, J Gregory Caporaso
Published 2021-06-01

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

by Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E. Diner, Gibraan Rahman, Daniel McDonald, George Armstrong, Sho Kodera, Sonya Donato, Gertrude Ecklu-Mensah, Neil Gottel, Mariana C. Salas Garcia, Leslie Y. Chiang, Rodolfo A. Salido, Justin P. Shaffer, Mac Kenzie Bryant, Karenina Sanders, Greg Humphrey, Gail Ackermann, Niina Haiminen, Kristen L. Beck, Ho-Cheol Kim, Anna Paola Carrieri, Laxmi Parida, Yoshiki Vázquez-Baeza, Francesca J. Torriani, Rob Knight, Jack Gilbert, Daniel A. Sweeney, Sarah M. Allard
Published 2021-06-01

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, The American Gut Consortium, Rob Knight
Published 2018-05-01