Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
Mills, Robert H, Dulai, Parambir S, Vázquez-Baeza, Yoshiki, Sauceda, Consuelo, Daniel, Noëmie, Gerner, Romana R, Batachari, Lakshmi E, Malfavon, Mario, Zhu, Qiyun, Weldon, Kelly, Humphrey, Greg, Carrillo-Terrazas, Marvic, Goldasich, Lindsay DeRight, Bryant, MacKenzie, Raffatellu, Manuela, Quinn, Robert A, Gewirtz, Andrew T, Chassaing, Benoit, Chu, Hiutung, Sandborn, William J, Dorrestein, Pieter C, Knight, Rob, Gonzalez, David J
Published in Nature microbiology (01.02.2022)
Published in Nature microbiology (01.02.2022)
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Journal Article
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Mu, Andre, McDonald, Daniel, Jarmusch, Alan K, Martino, Cameron, Brennan, Caitriona, Bryant, Mackenzie, Humphrey, Gregory C, Toronczak, Julia, Schwartz, Tara, Nguyen, Dominic, Ackermann, Gail, D'Onofrio, Anthony, Strathdee, Steffanie A, Schooley, Robert T, Dorrestein, Pieter C, Knight, Rob, Aslam, Saima
Published in Microbiome (14.04.2021)
Published in Microbiome (14.04.2021)
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Journal Article
Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection
Wang, Zheng, Peters, Brandilyn A, Bryant, MacKenzie, Hanna, David B, Schwartz, Tara, Wang, Tao, Sollecito, Christopher C, Usyk, Mykhaylo, Grassi, Evan, Wiek, Fanua, Peter, Lauren St, Post, Wendy S, Landay, Alan L, Hodis, Howard N, Weber, Kathleen M, French, Audrey, Golub, Elizabeth T, Lazar, Jason, Gustafson, Deborah, Sharma, Anjali, Anastos, Kathryn, Clish, Clary B, Burk, Robert D, Kaplan, Robert C, Knight, Rob, Qi, Qibin
Published in Microbiome (27.05.2023)
Published in Microbiome (27.05.2023)
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Journal Article
Enhancing untargeted metabolomics using metadata-based source annotation
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, Jr, 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
Published in Nature biotechnology (01.12.2022)
Published in Nature biotechnology (01.12.2022)
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Journal Article
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities
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
Published in BioTechniques (01.06.2022)
Published in BioTechniques (01.06.2022)
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Journal Article
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity
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
Published in Nature microbiology (01.12.2022)
Published in Nature microbiology (01.12.2022)
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Journal Article
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
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
Published in BioTechniques (01.03.2021)
Published in BioTechniques (01.03.2021)
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Journal Article
Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus)
Tang-Wing, Cassandra, Mohanty, Ipsita, Bryant, MacKenzie, Makowski, Katherine, Melendez, Daira, Dorrestein, Pieter C., Knight, Rob, Caraballo-Rodríguez, Andrés Mauricio, Allaband, Celeste, Jenné, Keith
Published in mSystems (20.08.2024)
Published in mSystems (20.08.2024)
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Journal Article
Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure
Cadena, Anthony M, Ma, Yixuan, Ding, Tao, Bryant, MacKenzie, Maiello, Pauline, Geber, Adam, Lin, Philana Ling, Flynn, JoAnne L, Ghedin, Elodie
Published in Microbiome (09.10.2018)
Published in Microbiome (09.10.2018)
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Journal Article
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution
Brennan, Caitriona, Salido, Rodolfo A, Belda-Ferre, Pedro, Bryant, MacKenzie, Cowart, Charles, Tiu, Maria D, González, Antonio, McDonald, Daniel, Tribelhorn, Caitlin, Zarrinpar, Amir, Knight, Rob
Published in mSystems (31.08.2023)
Published in mSystems (31.08.2023)
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Journal Article
Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses
Kumar, Tanya, Bryant, MacKenzie, Cantrell, Kalen, Song, Se Jin, McDonald, Daniel, Tubb, Helena M, Farmer, Sawyer, Lukacz, Emily S, Brubaker, Linda, Knight, Rob
Published in mSystems (23.02.2023)
Published in mSystems (23.02.2023)
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Journal Article
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights
Oles, Renee E., Carrillo Terrazas, Marvic, Loomis, Luke R., Hsu, Chia-Yun, Tribelhorn, Caitlin, Belda-Ferre, Pedro, Ea, Allison C., Bryant, MacKenzie, Young, Jocelyn A., Carrow, Hannah C., Sandborn, William J., Dulai, Parambir S., Sivagnanam, Mamata, Pride, David, Knight, Rob, Chu, Hiutung
Published in mSystems (23.07.2024)
Published in mSystems (23.07.2024)
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Journal Article
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
Marotz, Clarisse, Cavagnero, Kellen J, Song, Se Jin, McDonald, Daniel, Wandro, Stephen, Humphrey, Greg, Bryant, MacKenzie, Ackermann, Gail, Diaz, Edgar, Knight, Rob
Published in mSystems (27.04.2021)
Published in mSystems (27.04.2021)
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Journal Article
Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses
Kumar, Tanya, Bryant, MacKenzie, Cantrell, Kalen, Song, Se Jin, McDonald, Daniel, Tubb, Helena M, Farmer, Sawyer, Lewis, Amanda, Lukacz, Emily S, Brubaker, Linda, Knight, Rob
Published in Microbiology spectrum (11.01.2024)
Published in Microbiology spectrum (11.01.2024)
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Journal Article
Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
Taylor, Bryn C, Weldon, Kelly C, Ellis, Ronald J, Franklin, Donald, Groth, Tobin, Gentry, Emily C, Tripathi, Anupriya, McDonald, Daniel, Humphrey, Gregory, Bryant, MacKenzie, Toronczak, Julia, Schwartz, Tara, Oliveira, Michelli F, Heaton, Robert, Grant, Igor, Gianella, Sara, Letendre, Scott, Swafford, Austin, Dorrestein, Pieter C, Knight, Rob
Published in mSystems (29.09.2020)
Published in mSystems (29.09.2020)
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Journal Article
Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV
Taylor, Bryn C, Weldon, Kelly C, Ellis, Ronald J, Franklin, Donald, McDonald, Daniel, Humphrey, Gregory, Bryant, MacKenzie, Toronczak, Julia, Schwartz, Tara, Iudicello, Jennifer, Heaton, Robert, Grant, Igor, Gianella, Sara, Letendre, Scott, Swafford, Austin, Dorrestein, Pieter C, Knight, Rob
Published in mSystems (13.10.2020)
Published in mSystems (13.10.2020)
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Journal Article
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
Marotz, Clarisse, Cavagnero, Kellen J., Song, Se Jin, McDonald, Daniel, Wandro, Stephen, Humphrey, Greg, Bryant, MacKenzie, Ackermann, Gail, Diaz, Edgar, Knight, Rob
Published in mSystems (27.04.2021)
Published in mSystems (27.04.2021)
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Journal Article
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights
Oles, Renee E, Marvic Carrillo Terrazas, Loomis, Luke R, Chia-Yun Hsu, Tribelhorn, Caitlin, Pedro Belda Ferre, Ea, Allison, Mackenzie, Bryant, Young, Jocelyn, Carrow, Hannah C, Sandborn, William J, Dulai, Parambir, Sivagnanam, Mamata, Pride, David T, Knight, Rob, Chu, Hiutung
Published in bioRxiv (21.12.2023)
Published in bioRxiv (21.12.2023)
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Sa1881 COMPOSITION, FUNCTION, AND RHYTHMICITY OF THE GUT MICROBIOME IN A MOUSE MODEL OF ALZHEIMER'S DISEASE
Maissy, Erica S., Whittaker, Daniel S., Akhmetova, Laila, Richter, Alexander, Bryant, MacKenzie, Knight, Rob, Desplats, Paula, Zarrinpar, Amir
Published in Gastroenterology (New York, N.Y. 1943) (01.05.2023)
Published in Gastroenterology (New York, N.Y. 1943) (01.05.2023)
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Journal Article
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
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
Published in bioRxiv (14.11.2020)
Published in bioRxiv (14.11.2020)
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