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

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

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

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An Endohyphal Bacterium ( Chitinophaga , Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum ( F. solani Species Complex, Nectriaceae) von Shaffer, Justin P, U'Ren, Jana M, Gallery, Rachel E, Baltrus, David A, Arnold, A Elizabeth

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

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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 von Bailey, Maximilian J., Holzhausen, Elizabeth A., Morgan, Zachariah E. M., Naik, Noopur, Shaffer, Justin P., Liang, Donghai, Chang, Howard H., Sarnat, Jeremy, Sun, Shan, Berger, Paige K., Schmidt, Kelsey A., Lurmann, Frederick, Goran, Michael I., Alderete, Tanya L.

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

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Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California von Alderete, Tanya L., Jones, Roshonda B., Shaffer, Justin P., Holzhausen, Elizabeth A., Patterson, William B., Kazemian, Elham, Chatzi, Lida, Knight, Rob, Plows, Jasmine F., Berger, Paige K., Goran, Michael I.

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

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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment von Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., Allard, Sarah M.

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

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Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions von Narunsky-Haziza, Lian, Sepich-Poore, Gregory D, Livyatan, Ilana, Asraf, Omer, Martino, Cameron, Nejman, Deborah, Gavert, Nancy, Stajich, Jason E, Amit, Guy, González, Antonio, Wandro, Stephen, Perry, Gili, Ariel, Ruthie, Meltser, Arnon, Shaffer, Justin P, Zhu, Qiyun, Balint-Lahat, Nora, Barshack, Iris, Dadiani, Maya, Gal-Yam, Einav N, Patel, Sandip Pravin, Bashan, Amir, Swafford, Austin D, Pilpel, Yitzhak, Knight, Rob, Straussman, Ravid

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

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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 von Minich, Jeremiah J, Ali, Farhana, Marotz, Clarisse, Belda-Ferre, Pedro, Chiang, Leslie, Shaffer, Justin P, Carpenter, Carolina S, McDonald, Daniel, Gilbert, Jack, Allard, Sarah M, Allen, Eric E, Knight, Rob, Sweeney, Daniel A, Swafford, Austin D

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

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

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

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Enhancing untargeted metabolomics using metadata-based source annotation von Gauglitz, Julia M., West, Kiana A., Bittremieux, Wout, Williams, Candace L., Weldon, Kelly C., Panitchpakdi, Morgan, Di Ottavio, Francesca, Aceves, Christine M., Brown, Elizabeth, Sikora, Nicole C., Jarmusch, Alan K., Martino, Cameron, Tripathi, Anupriya, Meehan, Michael J., Dorrestein, Kathleen, Shaffer, Justin P., Coras, Roxana, Vargas, Fernando, Goldasich, Lindsay DeRight, Schwartz, Tara, Bryant, MacKenzie, Humphrey, Gregory, Johnson, Abigail J., Spengler, Katharina, Belda-Ferre, Pedro, Diaz, Edgar, McDonald, Daniel, Zhu, Qiyun, Elijah, Emmanuel O., Wang, Mingxun, Marotz, Clarisse, Sprecher, Kate E., Vargas-Robles, Daniela, Withrow, Dana, Ackermann, Gail, Herrera, Lourdes, Bradford, Barry J., Marques, Lucas Maciel Mauriz, Amaral, Juliano Geraldo, Silva, Rodrigo Moreira, Veras, Flavio Protasio, Cunha, Thiago Mattar, Oliveira, Rene Donizeti Ribeiro, Louzada-Junior, Paulo, Mills, Robert H., Piotrowski, Paulina K., Servetas, Stephanie L., Da Silva, Sandra M., Jones, Christina M., Lin, Nancy J., Lippa, Katrice A., Jackson, Scott A., Daouk, Rima Kaddurah, Galasko, Douglas, Dulai, Parambir S., Kalashnikova, Tatyana I., Wittenberg, Curt, Terkeltaub, Robert, Doty, Megan M., Kim, Jae H., Rhee, Kyung E., Beauchamp-Walters, Julia, Wright, Kenneth P., Dominguez-Bello, Maria Gloria, Manary, Mark, Oliveira, Michelli F., Boland, Brigid S., Lopes, Norberto Peporine, Guma, Monica, Swafford, Austin D., Dutton, Rachel J., Knight, Rob, Dorrestein, Pieter C.

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Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity von Shaffer, Justin P., Nothias, Louis-Félix, Thompson, Luke R., Sanders, Jon G., Salido, Rodolfo A., Couvillion, Sneha P., Brejnrod, Asker D., Lejzerowicz, Franck, Haiminen, Niina, Huang, Shi, Lutz, Holly L., Zhu, Qiyun, Martino, Cameron, Morton, James T., Karthikeyan, Smruthi, Nothias-Esposito, Mélissa, Dührkop, Kai, Böcker, Sebastian, Kim, Hyun Woo, Aksenov, Alexander A., Bittremieux, Wout, Minich, Jeremiah J., Marotz, Clarisse, Bryant, MacKenzie M., Sanders, Karenina, Schwartz, Tara, Humphrey, Greg, Vásquez-Baeza, Yoshiki, Tripathi, Anupriya, Parida, Laxmi, Carrieri, Anna Paola, Beck, Kristen L., Das, Promi, González, Antonio, McDonald, Daniel, Ladau, Joshua, Karst, Søren M., Albertsen, Mads, Ackermann, Gail, DeReus, Jeff, Thomas, Torsten, Petras, Daniel, Shade, Ashley, Stegen, James, Song, Se Jin, Metz, Thomas O., Swafford, Austin D., Dorrestein, Pieter C., Jansson, Janet K., Gilbert, Jack A., Knight, Rob

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

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