An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform von Fadrosh, Douglas W, Ma, Bing, Gajer, Pawel, Sengamalay, Naomi, Ott, Sandra, Brotman, Rebecca M, Ravel, Jacques

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Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis von McCauley, Kathryn E., DeMuri, Gregory, Lynch, Kole, Fadrosh, Douglas W., Santee, Clark, Nagalingam, Nabeetha N., Wald, Ellen R., Lynch, Susan V.

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Metagenomic exploration of viruses throughout the Indian Ocean von Williamson, Shannon J, Allen, Lisa Zeigler, Lorenzi, Hernan A, Fadrosh, Douglas W, Brami, Daniel, Thiagarajan, Mathangi, McCrow, John P, Tovchigrechko, Andrey, Yooseph, Shibu, Venter, J Craig

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Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis von Ravel, Jacques, Brotman, Rebecca M, Gajer, Pawel, Ma, Bing, Nandy, Melissa, Fadrosh, Douglas W, Sakamoto, Joyce, Koenig, Sara Sk, Fu, Li, Zhou, Xia, Hickey, Roxana J, Schwebke, Jane R, Forney, Larry J

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Gut-Resident Lactobacillus Abundance Associates with IDO1 Inhibition and Th17 Dynamics in SIV-Infected Macaques von Vujkovic-Cvijin, Ivan, Swainson, Louise A., Chu, Simon N., Ortiz, Alexandra M., Santee, Clark A., Petriello, Annalise, Dunham, Richard M., Fadrosh, Douglas W., Lin, Din L., Faruqi, Ali A., Huang, Yong, Apetrei, Cristian, Pandrea, Ivona, Hecht, Frederick M., Pilcher, Christopher D., Klatt, Nichole R., Brenchley, Jason M., Lynch, Susan V., McCune, Joseph M.

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Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls von Tremlett, Helen, Fadrosh, Douglas W, Faruqi, Ali A, Hart, Janace, Roalstad, Shelly, Graves, Jennifer, Spencer, Collin M, Lynch, Susan V, Zamvil, Scott S, Waubant, Emmanuelle

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Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment von Eloe, Emiley A., Shulse, Christine N., Fadrosh, Douglas W., Williamson, Shannon J., Allen, Eric E., Bartlett, Douglas H.

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Going deeper: metagenome of a hadopelagic microbial community von Eloe, Emiley A, Fadrosh, Douglas W, Novotny, Mark, Zeigler Allen, Lisa, Kim, Maria, Lombardo, Mary-Jane, Yee-Greenbaum, Joyclyn, Yooseph, Shibu, Allen, Eric E, Lasken, Roger, Williamson, Shannon J, Bartlett, Douglas H

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Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages von ANDREWS-PFANNKOCH, Cynthia, FADROSH, Douglas W, THORPE, Joyce, WILLIAMSON, Shannon J

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Distinct lung microbiota associate with HIV-associated chronic lung disease in children von Bhadriraju, Sudha, Fadrosh, Douglas W., Shenoy, Meera K., Lin, Din L., Lynch, Kole V., McCauley, Kathryn, Ferrand, Rashida A., Majonga, Edith D., McHugh, Grace, Huang, Laurence, Lynch, Susan V., Metcalfe, John Z.

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Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury von Howard, Benjamin M, Kornblith, Lucy Z, Christie, Sabrinah A, Conroy, Amanda S, Nelson, Mary F, Campion, Eric M, Callcut, Rachael A, Calfee, Carolyn S, Lamere, Brandon J, Fadrosh, Douglas W, Lynch, Susan, Cohen, Mitchell Jay

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Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction von Shenoy, Meera K, Fadrosh, Douglas W, Lin, Din L, Worodria, William, Byanyima, Patrick, Musisi, Emmanuel, Kaswabuli, Sylvia, Zawedde, Josephine, Sanyu, Ingvar, Chang, Emily, Fong, Serena, McCauley, Kathryn, Davis, J Lucian, Huang, Laurence, Lynch, Susan V

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Gut microbiota in early pediatric multiple sclerosis: a case−control study von Tremlett, H., Fadrosh, D. W., Faruqi, A. A., Zhu, F., Hart, J., Roalstad, S., Graves, J., Lynch, S., Waubant, E.

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The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women von Romero, Roberto, Hassan, Sonia S, Gajer, Pawel, Tarca, Adi L, Fadrosh, Douglas W, Nikita, Lorraine, Galuppi, Marisa, Lamont, Ronald F, Chaemsaithong, Piya, Miranda, Jezid, Chaiworapongsa, Tinnakorn, Ravel, Jacques

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Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma von McCauley, Kathryn, Durack, Juliana, Valladares, Ricardo, Fadrosh, Douglas W., Lin, Din L., Calatroni, Agustin, LeBeau, Petra K., Tran, Hoang T., Fujimura, Kei E., LaMere, Brandon, Merana, Geil, Lynch, Kole, Cohen, Robyn T., Pongracic, Jacqueline, Khurana Hershey, Gurjit K., Kercsmar, Carolyn M., Gill, Michelle, Liu, Andrew H., Kim, Haejin, Kattan, Meyer, Teach, Stephen J., Togias, Alkis, Boushey, Homer A., Gern, James E., Jackson, Daniel J., Lynch, Susan V.

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The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term von Romero, Roberto, Hassan, Sonia S, Gajer, Pawel, Tarca, Adi L, Fadrosh, Douglas W, Bieda, Janine, Chaemsaithong, Piya, Miranda, Jezid, Chaiworapongsa, Tinnakorn, Ravel, Jacques

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Gut microbiota composition and relapse risk in pediatric MS: A pilot study von Tremlett, Helen, Fadrosh, Douglas W, Faruqi, Ali A, Hart, Janace, Roalstad, Shelly, Graves, Jennifer, Lynch, Susan, Waubant, Emmanuelle

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Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations von McCauley, Kathryn E., Flynn, Kaitlin, Calatroni, Agustin, DiMassa, Vincent, LaMere, Brandon, Fadrosh, Douglas W., Lynch, Kole V., Gill, Michelle A., Pongracic, Jacqueline A., Khurana Hershey, Gurjit K., Kercsmar, Carolyn M., Liu, Andrew H., Johnson, Christine C., Kim, Haejin, Kattan, Meyer, O’Connor, George T., Bacharier, Leonard B., Teach, Stephen J., Gergen, Peter J., Wheatley, Lisa M., Togias, Alkis, LeBeau, Petra, Presnell, Scott, Boushey, Homer A., Busse, William W., Gern, James E., Jackson, Daniel J., Altman, Matthew C., Lynch, Susan V.

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Longitudinal Phenotypes of Respiratory Health in a High-Risk Urban Birth Cohort von Bacharier, Leonard B, Beigelman, Avraham, Calatroni, Agustin, Jackson, Daniel J, Gergen, Peter J, O'Connor, George T, Kattan, Meyer, Wood, Robert A, Sandel, Megan T, Lynch, Susan V, Fujimura, Kei E, Fadrosh, Douglas W, Santee, Clark A, Boushey, Homer, Visness, Cynthia M, Gern, James E

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Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus von Desjardins, Christopher A, Gundersen-Rindal, Dawn E, Hostetler, Jessica B, Tallon, Luke J, Fuester, Roger W, Schatz, Michael C, Pedroni, Monica J, Fadrosh, Douglas W, Haas, Brian J, Toms, Bradley S, Chen, Dan, Nene, Vishvanath

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