Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants. by Yue M Li, Justin P Shaffer, Brenna Hall, Hongseok Ko

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Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth R... by Justin P. Shaffer, Morgan E. Carter, Joseph E. Spraker, Meara Clark, Brian A. Smith, Kevin L. Hockett, David A. Baltrus, A. Elizabeth Arnold

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Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype by Cameron Martino, Daniel McDonald, Kalen Cantrell, Amanda Hazel Dilmore, Yoshiki Vázquez-Baeza, Liat Shenhav, Justin P. Shaffer, Gibraan Rahman, George Armstrong, Celeste Allaband, Se Jin Song, Rob Knight

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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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Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome by Bryn C. Taylor, Franck Lejzerowicz, Marion Poirel, Justin P. Shaffer, Lingjing Jiang, Alexander Aksenov, Nicole Litwin, Gregory Humphrey, Cameron Martino, Sandrine Miller-Montgomery, Pieter C. Dorrestein, Patrick Veiga, Se Jin Song, Daniel McDonald, Muriel Derrien, Rob Knight

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Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age by Maximilian J. Bailey, Elizabeth A. Holzhausen, Zachariah E. M. Morgan, Noopur Naik, Justin P. Shaffer, Donghai Liang, Howard H. Chang, Jeremy Sarnat, Shan Sun, Paige K. Berger, Kelsey A. Schmidt, Frederick Lurmann, Michael I. Goran, Tanya L. Alderete

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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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Peripheral neuronal activation shapes the microbiome and alters gut physiology by Jessica A. Griffiths, Bryan B. Yoo, Peter Thuy-Boun, Victor J. Cantu, Kelly C. Weldon, Collin Challis, Michael J. Sweredoski, Ken Y. Chan, Taren M. Thron, Gil Sharon, Annie Moradian, Gregory Humphrey, Qiyun Zhu, Justin P. Shaffer, Dennis W. Wolan, Pieter C. Dorrestein, Rob Knight, Viviana Gradinaru, Sarkis K. Mazmanian

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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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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

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Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities by Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh

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