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1. FDA/Arthritis Foundation osteoarthritis drug development workshop recap: Assessment of long-term benefit.

Author: Kim, Jason S, Kim, Jason S, Borges, Silvana, Clauw, Daniel J, Conaghan, Philip G, Felson, David T, Fleming, Thomas R, Glaser, Rachel, Hart, Elizabeth, Hochberg, Marc, Kim, Yura, Kraus, Virginia B, Lapteva, Larissa, Li, Xiaojuan, Majumdar, Sharmila, McAlindon, Timothy E, Mobasheri, Ali, Neogi, Tuhina, Roemer, Frank W, Rothwell, Rebecca, Shibuya, Robert, Siegel, Jeffrey, Simon, Lee S, Spindler, Kurt P, Nikolov, Nikolay P, Kim, Jason S, Kim, Jason S, Borges, Silvana, Clauw, Daniel J, Conaghan, Philip G, Felson, David T, Fleming, Thomas R, Glaser, Rachel, Hart, Elizabeth, Hochberg, Marc, Kim, Yura, Kraus, Virginia B, Lapteva, Larissa, Li, Xiaojuan, Majumdar, Sharmila, McAlindon, Timothy E, Mobasheri, Ali, Neogi, Tuhina, Roemer, Frank W, Rothwell, Rebecca, Shibuya, Robert, Siegel, Jeffrey, Simon, Lee S, Spindler, Kurt P, and Nikolov, Nikolay P
Abstract: ObjectiveTo summarize proceedings of a workshop convened to discuss the current state of science in the disease of osteoarthritis (OA), identify the knowledge gaps, and examine the developmental and regulatory challenges in bringing these products to market.DesignSummary of the one-day workshop held virtually on June 22nd, 2021.ResultsSpeakers selected by the Planning Committee presented data on the current approach to assessment of OA therapies, biomarkers in OA drug development, and the assessment of disease progression and long-term benefit.ConclusionsDemonstrated by numerous failed clinical trials, OA is a challenging disease for which to develop therapeutics. The challenge is magnified by the slow time of onset of disease and the need for clinical trials of long duration and/or large sample size to demonstrate the effect of an intervention. The OA science community, including academia, pharmaceutical companies, regulatory agencies, and patient communities, must continue to develop and test better clinical endpoints that meaningfully reflect disease modification related to long-term patient benefit.
Published: 2022

2. Electrostatic precipitators as an indoor air cleaner— a literature review

Author: Afshari, Alireza, Ekberg, Lars, Forejt, Luboš, Mo, Jinhan, Rahimi, Siamak, Siegel, Jeffrey, Chen, Wenhao, Wargocki, Pawel, Zurami, Sultan, Zhang, Jianshun, Afshari, Alireza, Ekberg, Lars, Forejt, Luboš, Mo, Jinhan, Rahimi, Siamak, Siegel, Jeffrey, Chen, Wenhao, Wargocki, Pawel, Zurami, Sultan, and Zhang, Jianshun
Abstract: Many people spend most of their time in an indoor environment. There is a positive relationship between indoor environmental quality and the health, wellbeing, and productivity of occupants in buildings. The indoor environment is affected by pollutants, such as gases and particles. Pollutants can be removed from the indoor environment in various ways. Air cleaning devices are commonly marketed as benefitting the removal of air pollutants and consequently, improving indoor air quality. Depending on the type of cleaning technology, air cleaners may generate undesired and toxic by-products. Different air filtration technologies such as electrostatic precipitators have been introduced to the market. The electrostatic precipitator (ESP) has been used in buildings because it can remove particles while only causes low pressure drops. Electrostatic precipitators can be either in-duct or standalone units. This review aims to give an overview of ESP use, methods for testing this product, the performance of existing ESPs in removing pollutants, their by-products, and the existing market for ESPs.
Published: 2020

3. Tocilizumab in systemic sclerosis:a randomised, double-blind, placebo-controlled, phase 3 trial

Author: Khanna, Dinesh, Lin, Celia J.F., Furst, Daniel E., Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M., Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P., Lucero, Eleonora, Pons-Estel, Bernardo, Rivero, Mariano, Tate, Guillermo, Smith, Vanessa, De Langhe, Ellen, Rashkov, Rasho, Batalov, Anastas, Goranov, Ivan, Stoilov, Rumen, Dunne, James, Johnson, Sindhu R., Pope, Janet E., Martinović Kaliterna, Dušanka, Mogensen, Mette, Olesen, Anne Braae, Henes, Joerg Christoph, Müller-Ladner, Ulf, Riemekasten, Gabriela, Skapenko, Alla, Vlachoyiannopoulos, Panayiotis, Kiss, Emese, Minier, Tünde, Beretta, Lorenzo, Gremese, Elisa, Valentini, Gabriele, Asano, Yoshihide, Atsumi, Tatsuya, Ihn, Hironobu, Ishii, Tomonori, Ishikawa, Osamu, Takahashi, Hiroki, Takehara, Kazuhiko, Tanaka, Yoshiya, Yamasaki, Yoshioki, Bukauskiene, Loreta, Butrimiene, Irena, Medrano Ramirez, Gabriel, Ramos-Remus, Cesar, Sofia Rodriguez Reyna, Tatiana, de Vries-Bouwstra, Jeska, Batko, Bogdan, Jeka, Slawomir, Kucharz, Eugeniusz, Majdan, Maria, Olesinska, Marzena, Smolenska, Zaneta, Alves, Jose, Santos, Maria, Mihai, Carmen Marina, Rednic, Simona, Castellvi Barranco, Ivan, Lopez Longo, Francisco Javier, Simeon Aznar, Carmen, Carreira, Patricia, Walker, Ulrich A., Derrett-Smith, Emma, Griffiths, Bridget, McKay, Neil, Aelion, Jacob, Borofsky, Michael, Fleischmann, Roy, Forstot, Joseph Z., Kafaja, Suzanne, Khan, M. Faisal, Kohen, Michael D., Martin, Richard W., Mendoza-Ballesteros, Fabian, Nami, Alireza, Pang, Shirley, Rios, Grissel, Simms, Robert, Sullivan, Keith Michael, Steen, Virginia D., Khanna, Dinesh, Lin, Celia J.F., Furst, Daniel E., Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M., Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P., Lucero, Eleonora, Pons-Estel, Bernardo, Rivero, Mariano, Tate, Guillermo, Smith, Vanessa, De Langhe, Ellen, Rashkov, Rasho, Batalov, Anastas, Goranov, Ivan, Stoilov, Rumen, Dunne, James, Johnson, Sindhu R., Pope, Janet E., Martinović Kaliterna, Dušanka, Mogensen, Mette, Olesen, Anne Braae, Henes, Joerg Christoph, Müller-Ladner, Ulf, Riemekasten, Gabriela, Skapenko, Alla, Vlachoyiannopoulos, Panayiotis, Kiss, Emese, Minier, Tünde, Beretta, Lorenzo, Gremese, Elisa, Valentini, Gabriele, Asano, Yoshihide, Atsumi, Tatsuya, Ihn, Hironobu, Ishii, Tomonori, Ishikawa, Osamu, Takahashi, Hiroki, Takehara, Kazuhiko, Tanaka, Yoshiya, Yamasaki, Yoshioki, Bukauskiene, Loreta, Butrimiene, Irena, Medrano Ramirez, Gabriel, Ramos-Remus, Cesar, Sofia Rodriguez Reyna, Tatiana, de Vries-Bouwstra, Jeska, Batko, Bogdan, Jeka, Slawomir, Kucharz, Eugeniusz, Majdan, Maria, Olesinska, Marzena, Smolenska, Zaneta, Alves, Jose, Santos, Maria, Mihai, Carmen Marina, Rednic, Simona, Castellvi Barranco, Ivan, Lopez Longo, Francisco Javier, Simeon Aznar, Carmen, Carreira, Patricia, Walker, Ulrich A., Derrett-Smith, Emma, Griffiths, Bridget, McKay, Neil, Aelion, Jacob, Borofsky, Michael, Fleischmann, Roy, Forstot, Joseph Z., Kafaja, Suzanne, Khan, M. Faisal, Kohen, Michael D., Martin, Richard W., Mendoza-Ballesteros, Fabian, Nami, Alireza, Pang, Shirley, Rios, Grissel, Simms, Robert, Sullivan, Keith Michael, and Steen, Virginia D.
Abstract: Background: A phase 2 trial of tocilizumab showed preliminary evidence of efficacy in systemic sclerosis. We assessed skin fibrosis and systemic sclerosis-associated interstitial lung disease (SSc-ILD) in a phase 3 trial to investigate the safety and efficacy of tocilizumab, an anti-interleukin-6 receptor antibody, in the treatment of systemic sclerosis. Methods: In this multicentre, randomised, double-blind, placebo-controlled, phase 3 trial, participants were recruited from 75 sites in 20 countries across Europe, North America, Latin America, and Japan. Adults with diffuse cutaneous systemic sclerosis for 60 months or less and a modified Rodnan skin score (mRSS) of 10–35 at screening were randomly assigned (1:1) with a voice-web-response system to receive subcutaneous tocilizumab 162 mg or placebo weekly for 48 weeks, stratified by IL-6 levels; participants and investigators were masked to treatment group. The primary endpoint was the difference in change from baseline to week 48 in mRSS. Percentage of predicted forced vital capacity (FVC% predicted) at week 48, time to treatment failure, and patient-reported and physician-reported outcomes were secondary endpoints. This trial is registered with ClinicalTrials.gov (number NCT02453256) and is closed to accrual. Findings: Between Nov 20, 2015, and Feb 14, 2017, 210 individuals were randomly assigned to receive tocilizumab (n=104) or placebo (n=106). In the intention-to-treat population, least squares mean [LSM] change from baseline to week 48 in mRSS was −6·14 for tocilizumab and −4·41 for placebo (adjusted difference −1·73 [95% CI −3·78 to 0·32]; p=0·10). The shift in distribution of change from baseline in FVC% predicted at week 48 favoured tocilizumab (van Elteren nominal p=0·002 vs placebo), with a difference in LSM of 4·2 (95% CI 2·0–6·4; nominal p=0·0002), as did time to treatment failure (hazard ratio 0·63 [95% CI 0·37–1·06]; nominal p=0·08). Change in LSM from baseline to week 48 in Health Assessment Ques
Published: 2020

4. Tocilizumab in systemic sclerosis:a randomised, double-blind, placebo-controlled, phase 3 trial

Author: Khanna, Dinesh, Lin, Celia J.F., Furst, Daniel E., Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M., Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P., Lucero, Eleonora, Pons-Estel, Bernardo, Rivero, Mariano, Tate, Guillermo, Smith, Vanessa, De Langhe, Ellen, Rashkov, Rasho, Batalov, Anastas, Goranov, Ivan, Stoilov, Rumen, Dunne, James, Johnson, Sindhu R., Pope, Janet E., Martinović Kaliterna, Dušanka, Mogensen, Mette, Olesen, Anne Braae, Henes, Joerg Christoph, Müller-Ladner, Ulf, Riemekasten, Gabriela, Skapenko, Alla, Vlachoyiannopoulos, Panayiotis, Kiss, Emese, Minier, Tünde, Beretta, Lorenzo, Gremese, Elisa, Valentini, Gabriele, Asano, Yoshihide, Atsumi, Tatsuya, Ihn, Hironobu, Ishii, Tomonori, Ishikawa, Osamu, Takahashi, Hiroki, Takehara, Kazuhiko, Tanaka, Yoshiya, Yamasaki, Yoshioki, Bukauskiene, Loreta, Butrimiene, Irena, Medrano Ramirez, Gabriel, Ramos-Remus, Cesar, Sofia Rodriguez Reyna, Tatiana, de Vries-Bouwstra, Jeska, Batko, Bogdan, Jeka, Slawomir, Kucharz, Eugeniusz, Majdan, Maria, Olesinska, Marzena, Smolenska, Zaneta, Alves, Jose, Santos, Maria, Mihai, Carmen Marina, Rednic, Simona, Castellvi Barranco, Ivan, Lopez Longo, Francisco Javier, Simeon Aznar, Carmen, Carreira, Patricia, Walker, Ulrich A., Derrett-Smith, Emma, Griffiths, Bridget, McKay, Neil, Aelion, Jacob, Borofsky, Michael, Fleischmann, Roy, Forstot, Joseph Z., Kafaja, Suzanne, Khan, M. Faisal, Kohen, Michael D., Martin, Richard W., Mendoza-Ballesteros, Fabian, Nami, Alireza, Pang, Shirley, Rios, Grissel, Simms, Robert, Sullivan, Keith Michael, Steen, Virginia D., Khanna, Dinesh, Lin, Celia J.F., Furst, Daniel E., Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M., Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P., Lucero, Eleonora, Pons-Estel, Bernardo, Rivero, Mariano, Tate, Guillermo, Smith, Vanessa, De Langhe, Ellen, Rashkov, Rasho, Batalov, Anastas, Goranov, Ivan, Stoilov, Rumen, Dunne, James, Johnson, Sindhu R., Pope, Janet E., Martinović Kaliterna, Dušanka, Mogensen, Mette, Olesen, Anne Braae, Henes, Joerg Christoph, Müller-Ladner, Ulf, Riemekasten, Gabriela, Skapenko, Alla, Vlachoyiannopoulos, Panayiotis, Kiss, Emese, Minier, Tünde, Beretta, Lorenzo, Gremese, Elisa, Valentini, Gabriele, Asano, Yoshihide, Atsumi, Tatsuya, Ihn, Hironobu, Ishii, Tomonori, Ishikawa, Osamu, Takahashi, Hiroki, Takehara, Kazuhiko, Tanaka, Yoshiya, Yamasaki, Yoshioki, Bukauskiene, Loreta, Butrimiene, Irena, Medrano Ramirez, Gabriel, Ramos-Remus, Cesar, Sofia Rodriguez Reyna, Tatiana, de Vries-Bouwstra, Jeska, Batko, Bogdan, Jeka, Slawomir, Kucharz, Eugeniusz, Majdan, Maria, Olesinska, Marzena, Smolenska, Zaneta, Alves, Jose, Santos, Maria, Mihai, Carmen Marina, Rednic, Simona, Castellvi Barranco, Ivan, Lopez Longo, Francisco Javier, Simeon Aznar, Carmen, Carreira, Patricia, Walker, Ulrich A., Derrett-Smith, Emma, Griffiths, Bridget, McKay, Neil, Aelion, Jacob, Borofsky, Michael, Fleischmann, Roy, Forstot, Joseph Z., Kafaja, Suzanne, Khan, M. Faisal, Kohen, Michael D., Martin, Richard W., Mendoza-Ballesteros, Fabian, Nami, Alireza, Pang, Shirley, Rios, Grissel, Simms, Robert, Sullivan, Keith Michael, and Steen, Virginia D.
Abstract: Background: A phase 2 trial of tocilizumab showed preliminary evidence of efficacy in systemic sclerosis. We assessed skin fibrosis and systemic sclerosis-associated interstitial lung disease (SSc-ILD) in a phase 3 trial to investigate the safety and efficacy of tocilizumab, an anti-interleukin-6 receptor antibody, in the treatment of systemic sclerosis. Methods: In this multicentre, randomised, double-blind, placebo-controlled, phase 3 trial, participants were recruited from 75 sites in 20 countries across Europe, North America, Latin America, and Japan. Adults with diffuse cutaneous systemic sclerosis for 60 months or less and a modified Rodnan skin score (mRSS) of 10–35 at screening were randomly assigned (1:1) with a voice-web-response system to receive subcutaneous tocilizumab 162 mg or placebo weekly for 48 weeks, stratified by IL-6 levels; participants and investigators were masked to treatment group. The primary endpoint was the difference in change from baseline to week 48 in mRSS. Percentage of predicted forced vital capacity (FVC% predicted) at week 48, time to treatment failure, and patient-reported and physician-reported outcomes were secondary endpoints. This trial is registered with ClinicalTrials.gov (number NCT02453256) and is closed to accrual. Findings: Between Nov 20, 2015, and Feb 14, 2017, 210 individuals were randomly assigned to receive tocilizumab (n=104) or placebo (n=106). In the intention-to-treat population, least squares mean [LSM] change from baseline to week 48 in mRSS was −6·14 for tocilizumab and −4·41 for placebo (adjusted difference −1·73 [95% CI −3·78 to 0·32]; p=0·10). The shift in distribution of change from baseline in FVC% predicted at week 48 favoured tocilizumab (van Elteren nominal p=0·002 vs placebo), with a difference in LSM of 4·2 (95% CI 2·0–6·4; nominal p=0·0002), as did time to treatment failure (hazard ratio 0·63 [95% CI 0·37–1·06]; nominal p=0·08). Change in LSM from baseline to week 48 in Health Assessment Ques
Published: 2020

5. Tocilizumab in systemic sclerosis: a randomised, double-blind, placebo-controlled, phase 3 trial

Author: MS Reumatologie/Immunologie/Infectie, Infection & Immunity, Regenerative Medicine and Stem Cells, Khanna, Dinesh, Lin, Celia J F, Furst, Daniel E, Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M, Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P, focuSSced investigators, MS Reumatologie/Immunologie/Infectie, Infection & Immunity, Regenerative Medicine and Stem Cells, Khanna, Dinesh, Lin, Celia J F, Furst, Daniel E, Goldin, Jonathan, Kim, Grace, Kuwana, Masataka, Allanore, Yannick, Matucci-Cerinic, Marco, Distler, Oliver, Shima, Yoshihito, van Laar, Jacob M, Spotswood, Helen, Wagner, Bridget, Siegel, Jeffrey, Jahreis, Angelika, Denton, Christopher P, and focuSSced investigators
Published: 2020

6. A communal catalogue reveals Earth's multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
Published: 2017
Full Text: View/download PDF

7. A communal catalogue reveals Earth’s multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Published: 2017
Full Text: View/download PDF

8. A communal catalogue reveals Earth's multiscale microbial diversity

Author: Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
Published: 2017

9. A communal catalogue reveals Earth’s multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Published: 2017
Full Text: View/download PDF

10. A communal catalogue reveals Earth’s multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Abstract: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Published: 2017
Full Text: View/download PDF

11. Integrating ducts into the conditioned space: Successes and challenges

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Siegel, Jeffrey, Siegel, Jeffrey, and Walker, Iain
Published: 2004

12. Integrating ducts into the conditioned space: Successes and challenges

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Siegel, Jeffrey, Siegel, Jeffrey, and Walker, Iain
Published: 2004

13. An evaluation of superheat-based refrigerant charge diagnostics for residential cooling systems

Author: Siegel, Jeffrey A., Siegel, Jeffrey A., Siegel, Jeffrey A., and Siegel, Jeffrey A.
Published: 2002

14. Dirty air conditioners: Energy implications of coil fouling

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Sherman, Max, Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, and Sherman, Max
Published: 2002

15. Comparison between predicted duct effectiveness from proposed ASHRAE Standard 152P and measured field data for residential forced air cooling systems

Author: Siegel, Jeffrey A., Siegel, Jeffrey A., McWilliams, Jennifer A., Walker, Iain S., Siegel, Jeffrey A., Siegel, Jeffrey A., McWilliams, Jennifer A., and Walker, Iain S.
Published: 2002

16. Dirty air conditioners: Energy implications of coil fouling

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Sherman, Max, Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, and Sherman, Max
Published: 2002

17. Comparison between predicted duct effectiveness from proposed ASHRAE Standard 152P and measured field data for residential forced air cooling systems

Author: Siegel, Jeffrey A., Siegel, Jeffrey A., McWilliams, Jennifer A., Walker, Iain S., Siegel, Jeffrey A., Siegel, Jeffrey A., McWilliams, Jennifer A., and Walker, Iain S.
Published: 2002

18. An evaluation of superheat-based refrigerant charge diagnostics for residential cooling systems

Author: Siegel, Jeffrey A., Siegel, Jeffrey A., Siegel, Jeffrey A., and Siegel, Jeffrey A.
Published: 2002

19. Geography and Location Are the Primary Drivers of Office Microbiome Composition.

Author: Chase, John, Chase, John, Fouquier, Jennifer, Zare, Mahnaz, Sonderegger, Derek L, Knight, Rob, Kelley, Scott T, Siegel, Jeffrey, Caporaso, J Gregory, Chase, John, Chase, John, Fouquier, Jennifer, Zare, Mahnaz, Sonderegger, Derek L, Knight, Rob, Kelley, Scott T, Siegel, Jeffrey, and Caporaso, J Gregory
Abstract: In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, distu
Published: 2016

20. Safety and efficacy of subcutaneous tocilizumab in adults with systemic sclerosis (faSScinate) : a phase 2, randomised, controlled trial

Author: Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, Furst, Daniel E., Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, and Furst, Daniel E.
Published: 2016

21. Safety and efficacy of subcutaneous tocilizumab in adults with systemic sclerosis (faSScinate) : a phase 2, randomised, controlled trial

Author: Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, Furst, Daniel E., Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, and Furst, Daniel E.
Published: 2016

22. Geography and Location Are the Primary Drivers of Office Microbiome Composition.

Author: Chase, John, Gilbert, Jack A1, Chase, John, Fouquier, Jennifer, Zare, Mahnaz, Sonderegger, Derek L, Knight, Rob, Kelley, Scott T, Siegel, Jeffrey, Caporaso, J Gregory, Chase, John, Gilbert, Jack A1, Chase, John, Fouquier, Jennifer, Zare, Mahnaz, Sonderegger, Derek L, Knight, Rob, Kelley, Scott T, Siegel, Jeffrey, and Caporaso, J Gregory
Abstract: In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, distu
Published: 2016

23. Safety and efficacy of subcutaneous tocilizumab in adults with systemic sclerosis (faSScinate) : a phase 2, randomised, controlled trial

Author: Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, Furst, Daniel E., Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, and Furst, Daniel E.
Published: 2016

24. The American College of Rheumatology Provisional Composite Response Index for Clinical Trials in Early Diffuse Cutaneous Systemic Sclerosis.

Author: Khanna, Dinesh, Khanna, Dinesh, Berrocal, Veronica J, Giannini, Edward H, Seibold, James R, Merkel, Peter A, Mayes, Maureen D, Baron, Murray, Clements, Philip J, Steen, Virginia, Assassi, Shervin, Schiopu, Elena, Phillips, Kristine, Simms, Robert W, Allanore, Yannick, Denton, Christopher P, Distler, Oliver, Johnson, Sindhu R, Matucci-Cerinic, Marco, Pope, Janet E, Proudman, Susanna M, Siegel, Jeffrey, Wong, Weng Kee, Wells, Athol U, Furst, Daniel E, Khanna, Dinesh, Khanna, Dinesh, Berrocal, Veronica J, Giannini, Edward H, Seibold, James R, Merkel, Peter A, Mayes, Maureen D, Baron, Murray, Clements, Philip J, Steen, Virginia, Assassi, Shervin, Schiopu, Elena, Phillips, Kristine, Simms, Robert W, Allanore, Yannick, Denton, Christopher P, Distler, Oliver, Johnson, Sindhu R, Matucci-Cerinic, Marco, Pope, Janet E, Proudman, Susanna M, Siegel, Jeffrey, Wong, Weng Kee, Wells, Athol U, and Furst, Daniel E
Abstract: ObjectiveEarly diffuse cutaneous systemic sclerosis (dcSSc) is characterized by rapid changes in the skin and internal organs. The objective of this study was to develop a composite response index in dcSSc (CRISS) for use in randomized controlled trials (RCTs).MethodsWe developed 150 paper patient profiles with standardized clinical outcome elements (core set items) using patients with dcSSc. Forty scleroderma experts rated 20 patient profiles each and assessed whether each patient had improved or not improved over a period of 1 year. Using the profiles for which raters had reached a consensus on whether the patients were improved versus not improved (79% of the profiles examined), we fit logistic regression models in which the binary outcome referred to whether the patient was improved or not, and the changes in the core set items from baseline to followup were entered as covariates. We tested the final index in a previously completed RCT.ResultsSixteen of 31 core items were included in the patient profiles after a consensus meeting and review of test characteristics of patient-level data. In the logistic regression model in which the included core set items were change over 1 year in the modified Rodnan skin thickness score, the forced vital capacity, the patient and physician global assessments, and the Health Assessment Questionnaire disability index, sensitivity was 0.982 (95% confidence interval 0.982-0.983) and specificity was 0.931 (95% confidence interval 0.930-0.932), and the model with these 5 items had the highest face validity. Subjects with a significant worsening of renal or cardiopulmonary involvement were classified as not improved, regardless of improvements in other core items. With use of the index, the effect of methotrexate could be differentiated from the effect of placebo in a 1-year RCT (P = 0.02).ConclusionWe have developed a CRISS that is appropriate for use as an outcome assessment in RCTs of early dcSSc.
Published: 2016

25. The American College of Rheumatology Provisional Composite Response Index for Clinical Trials in Early Diffuse Cutaneous Systemic Sclerosis.

Author: Khanna, Dinesh, Khanna, Dinesh, Berrocal, Veronica J, Giannini, Edward H, Seibold, James R, Merkel, Peter A, Mayes, Maureen D, Baron, Murray, Clements, Philip J, Steen, Virginia, Assassi, Shervin, Schiopu, Elena, Phillips, Kristine, Simms, Robert W, Allanore, Yannick, Denton, Christopher P, Distler, Oliver, Johnson, Sindhu R, Matucci-Cerinic, Marco, Pope, Janet E, Proudman, Susanna M, Siegel, Jeffrey, Wong, Weng Kee, Wells, Athol U, Furst, Daniel E, Khanna, Dinesh, Khanna, Dinesh, Berrocal, Veronica J, Giannini, Edward H, Seibold, James R, Merkel, Peter A, Mayes, Maureen D, Baron, Murray, Clements, Philip J, Steen, Virginia, Assassi, Shervin, Schiopu, Elena, Phillips, Kristine, Simms, Robert W, Allanore, Yannick, Denton, Christopher P, Distler, Oliver, Johnson, Sindhu R, Matucci-Cerinic, Marco, Pope, Janet E, Proudman, Susanna M, Siegel, Jeffrey, Wong, Weng Kee, Wells, Athol U, and Furst, Daniel E
Abstract: ObjectiveEarly diffuse cutaneous systemic sclerosis (dcSSc) is characterized by rapid changes in the skin and internal organs. The objective of this study was to develop a composite response index in dcSSc (CRISS) for use in randomized controlled trials (RCTs).MethodsWe developed 150 paper patient profiles with standardized clinical outcome elements (core set items) using patients with dcSSc. Forty scleroderma experts rated 20 patient profiles each and assessed whether each patient had improved or not improved over a period of 1 year. Using the profiles for which raters had reached a consensus on whether the patients were improved versus not improved (79% of the profiles examined), we fit logistic regression models in which the binary outcome referred to whether the patient was improved or not, and the changes in the core set items from baseline to followup were entered as covariates. We tested the final index in a previously completed RCT.ResultsSixteen of 31 core items were included in the patient profiles after a consensus meeting and review of test characteristics of patient-level data. In the logistic regression model in which the included core set items were change over 1 year in the modified Rodnan skin thickness score, the forced vital capacity, the patient and physician global assessments, and the Health Assessment Questionnaire disability index, sensitivity was 0.982 (95% confidence interval 0.982-0.983) and specificity was 0.931 (95% confidence interval 0.930-0.932), and the model with these 5 items had the highest face validity. Subjects with a significant worsening of renal or cardiopulmonary involvement were classified as not improved, regardless of improvements in other core items. With use of the index, the effect of methotrexate could be differentiated from the effect of placebo in a 1-year RCT (P = 0.02).ConclusionWe have developed a CRISS that is appropriate for use as an outcome assessment in RCTs of early dcSSc.
Published: 2016

26. Safety and efficacy of subcutaneous tocilizumab in adults with systemic sclerosis (faSScinate): a phase 2, randomised, controlled trial

Author: MS Reumatologie/Immunologie/Infectie, Infection & Immunity, Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, Furst, Daniel E., MS Reumatologie/Immunologie/Infectie, Infection & Immunity, Khanna, Dinesh, Denton, Christopher P., Jahreis, Angelika, van Laar, Jacob M., Frech, Tracy M., Anderson, Marina E., Baron, Murray, Chung, Lorinda, Fierlbeck, Gerhard, Lakshminarayanan, Santhanam, Allanore, Yannick, Pope, Janet E., Riemekasten, Gabriela, Steen, Virginia, Müller-Ladner, Ulf, Lafyatis, Robert, Stifano, Giuseppina, Spotswood, Helen, Chen-Harris, Haiyin, Dziadek, Sebastian, Morimoto, Alyssa, Sornasse, Thierry, Siegel, Jeffrey, and Furst, Daniel E.
Published: 2016

27. Deposition of biological aerosols on HVAC heat exchangers

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Siegel, Jeffrey, Siegel, Jeffrey, and Walker, Iain
Published: 2001

28. Fouling of HVAC fin and tube heat exchangers

Author: Siegel, Jeffrey, Siegel, Jeffrey, Carey, Van P., Siegel, Jeffrey, Siegel, Jeffrey, and Carey, Van P.
Published: 2001

29. Deposition of biological aerosols on HVAC heat exchangers

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Siegel, Jeffrey, Siegel, Jeffrey, and Walker, Iain
Published: 2001

30. Fouling of HVAC fin and tube heat exchangers

Author: Siegel, Jeffrey, Siegel, Jeffrey, Carey, Van P., Siegel, Jeffrey, Siegel, Jeffrey, and Carey, Van P.
Published: 2001

31. Delivering Tons to the Register: Energy Efficient Design and Operation of Residential Cooling Systems

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, lain, Sherman, Max, Siegel, Jeffrey, Siegel, Jeffrey, Walker, lain, and Sherman, Max
Published: 2000

32. Delivering tons to the register: Energy efficient design and operation of residential cooling systems

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Sherman, Max, Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, and Sherman, Max
Published: 2000

33. Delivering tons to the register: Energy efficient design and operation of residential cooling systems

Author: Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, Sherman, Max, Siegel, Jeffrey, Siegel, Jeffrey, Walker, Iain, and Sherman, Max
Published: 2000

34. Spatial and temporal variations in indoor environmental conditions, human occupancy, and operational characteristics in a new hospital building.

Author: Ramos, Tiffanie, Ramos, Tiffanie, Dedesko, Sandra, Siegel, Jeffrey A, Gilbert, Jack A, Stephens, Brent, Ramos, Tiffanie, Ramos, Tiffanie, Dedesko, Sandra, Siegel, Jeffrey A, Gilbert, Jack A, and Stephens, Brent
Abstract: The dynamics of indoor environmental conditions, human occupancy, and operational characteristics of buildings influence human comfort and indoor environmental quality, including the survival and progression of microbial communities. A suite of continuous, long-term environmental and operational parameters were measured in ten patient rooms and two nurse stations in a new hospital building in Chicago, IL to characterize the indoor environment in which microbial samples were taken for the Hospital Microbiome Project. Measurements included environmental conditions (indoor dry-bulb temperature, relative humidity, humidity ratio, and illuminance) in the patient rooms and nurse stations; differential pressure between the patient rooms and hallways; surrogate measures for human occupancy and activity in the patient rooms using both indoor air CO2 concentrations and infrared doorway beam-break counters; and outdoor air fractions in the heating, ventilating, and air-conditioning systems serving the sampled spaces. Measurements were made at 5-minute intervals over consecutive days for nearly one year, providing a total of ∼8×106 data points. Indoor temperature, illuminance, and human occupancy/activity were all weakly correlated between rooms, while relative humidity, humidity ratio, and outdoor air fractions showed strong temporal (seasonal) patterns and strong spatial correlations between rooms. Differential pressure measurements confirmed that all patient rooms were operated at neutral pressure. The patient rooms averaged about 100 combined entrances and exits per day, which suggests they were relatively lightly occupied compared to higher traffic environments (e.g., retail buildings) and more similar to lower traffic office environments. There were also clear differences in several environmental parameters before and after the hospital was occupied with patients and staff. Characterizing and understanding factors that influence these building dynamics is vital for hospit
Published: 2015

35. Spatial and temporal variations in indoor environmental conditions, human occupancy, and operational characteristics in a new hospital building.

Author: Ramos, Tiffanie, Morais, Paula V1, Ramos, Tiffanie, Dedesko, Sandra, Siegel, Jeffrey A, Gilbert, Jack A, Stephens, Brent, Ramos, Tiffanie, Morais, Paula V1, Ramos, Tiffanie, Dedesko, Sandra, Siegel, Jeffrey A, Gilbert, Jack A, and Stephens, Brent
Abstract: The dynamics of indoor environmental conditions, human occupancy, and operational characteristics of buildings influence human comfort and indoor environmental quality, including the survival and progression of microbial communities. A suite of continuous, long-term environmental and operational parameters were measured in ten patient rooms and two nurse stations in a new hospital building in Chicago, IL to characterize the indoor environment in which microbial samples were taken for the Hospital Microbiome Project. Measurements included environmental conditions (indoor dry-bulb temperature, relative humidity, humidity ratio, and illuminance) in the patient rooms and nurse stations; differential pressure between the patient rooms and hallways; surrogate measures for human occupancy and activity in the patient rooms using both indoor air CO2 concentrations and infrared doorway beam-break counters; and outdoor air fractions in the heating, ventilating, and air-conditioning systems serving the sampled spaces. Measurements were made at 5-minute intervals over consecutive days for nearly one year, providing a total of ∼8×106 data points. Indoor temperature, illuminance, and human occupancy/activity were all weakly correlated between rooms, while relative humidity, humidity ratio, and outdoor air fractions showed strong temporal (seasonal) patterns and strong spatial correlations between rooms. Differential pressure measurements confirmed that all patient rooms were operated at neutral pressure. The patient rooms averaged about 100 combined entrances and exits per day, which suggests they were relatively lightly occupied compared to higher traffic environments (e.g., retail buildings) and more similar to lower traffic office environments. There were also clear differences in several environmental parameters before and after the hospital was occupied with patients and staff. Characterizing and understanding factors that influence these building dynamics is vital for hospit
Published: 2015

36. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

Author: Smith, Daniel, Smith, Daniel, Alverdy, John, An, Gary, Coleman, Maureen, Garcia-Houchins, Sylvia, Green, Jessica, Keegan, Kevin, Kelley, Scott T, Kirkup, Benjamin C, Kociolek, Larry, Levin, Hal, Landon, Emily, Olsiewski, Paula, Knight, Rob, Siegel, Jeffrey, Weber, Stephen, Gilbert, Jack, Smith, Daniel, Smith, Daniel, Alverdy, John, An, Gary, Coleman, Maureen, Garcia-Houchins, Sylvia, Green, Jessica, Keegan, Kevin, Kelley, Scott T, Kirkup, Benjamin C, Kociolek, Larry, Levin, Hal, Landon, Emily, Olsiewski, Paula, Knight, Rob, Siegel, Jeffrey, Weber, Stephen, and Gilbert, Jack
Abstract: This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium.
Published: 2013

37. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

Author: Smith, Daniel, Smith, Daniel, Alverdy, John, An, Gary, Coleman, Maureen, Garcia-Houchins, Sylvia, Green, Jessica, Keegan, Kevin, Kelley, Scott T, Kirkup, Benjamin C, Kociolek, Larry, Levin, Hal, Landon, Emily, Olsiewski, Paula, Knight, Rob, Siegel, Jeffrey, Weber, Stephen, Gilbert, Jack, Smith, Daniel, Smith, Daniel, Alverdy, John, An, Gary, Coleman, Maureen, Garcia-Houchins, Sylvia, Green, Jessica, Keegan, Kevin, Kelley, Scott T, Kirkup, Benjamin C, Kociolek, Larry, Levin, Hal, Landon, Emily, Olsiewski, Paula, Knight, Rob, Siegel, Jeffrey, Weber, Stephen, and Gilbert, Jack
Abstract: This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium.
Published: 2013

38. Analysis of life cycle cost methods for heating, ventilation, and air conditioning systems in hospitals

Author: Siegel, Jeffrey A., University of Texas at Austin, Engineering, Krus, Christopher James, Siegel, Jeffrey A., University of Texas at Austin, Engineering, and Krus, Christopher James
Abstract: CIVINS (Civilian Institutions) Thesis document, The purpose of this research was to evaluate the current body of knowledge relating to life cycle costing of heating, ventilation and air conditioning systems (HVAC) systems in hospitals. Life cycle cost (LCC) is the total cost of procuring, designing, owning, operating, maintaining, and disposing of a building over its useful life (including its fuel and water, energy, labor, and replacement components), determined on the basis of a systematic evaluation and comparison. Both government and private hospitals were studied. Hospitals have several characteristics that made them useful to consider. They are: typically owned by either goverments or large corporations, regulated as a class, not solely driven by profitability or return on investment, financed over the long-term by bonding or taxes, expected to have long service lives, not likely to change building use and functions over time, often procured through processes open to public scrutiny, and operated by decision makers who are not facilities specialists. Evaluation of life cycle costs is important because the true costs of ownership of a facility are much larger than the initial construction cost investment. Initial cost is typically the subject of intense scrutiny during design and planning and HVAC systems represent significant portions of the initial cost of a facility and consequently involve significant design choices and trade-offs., http://archive.org/details/analysisoflifecy1094537781, Approved for public release; distribution is unlimited.
Published: 2013

39. Analysis of life cycle cost methods for heating, ventilation, and air conditioning systems in hospitals

Author: Siegel, Jeffrey A., University of Texas at Austin, Engineering, Krus, Christopher James, Siegel, Jeffrey A., University of Texas at Austin, Engineering, and Krus, Christopher James
Abstract: The purpose of this research was to evaluate the current body of knowledge relating to life cycle costing of heating, ventilation and air conditioning systems (HVAC) systems in hospitals. Life cycle cost (LCC) is the total cost of procuring, designing, owning, operating, maintaining, and disposing of a building over its useful life (including its fuel and water, energy, labor, and replacement components), determined on the basis of a systematic evaluation and comparison. Both government and private hospitals were studied. Hospitals have several characteristics that made them useful to consider. They are: typically owned by either goverments or large corporations, regulated as a class, not solely driven by profitability or return on investment, financed over the long-term by bonding or taxes, expected to have long service lives, not likely to change building use and functions over time, often procured through processes open to public scrutiny, and operated by decision makers who are not facilities specialists. Evaluation of life cycle costs is important because the true costs of ownership of a facility are much larger than the initial construction cost investment. Initial cost is typically the subject of intense scrutiny during design and planning and HVAC systems represent significant portions of the initial cost of a facility and consequently involve significant design choices and trade-offs.
Published: 2004

40. Distribution Effectiveness and Impacts on Equipment Sizing for Residential Thermal Distribution Systems

Author: Walker, Iain, Walker, Iain, Sherman, Max, Siegel, Jeffrey, Walker, Iain, Walker, Iain, Sherman, Max, and Siegel, Jeffrey
Published: 1999

41. Signal Transduction in T Cell Activation and Tolerance

Author: NAVAL MEDICAL RESEARCH INST BETHESDA MD, Siegel, Jeffrey N., June, Carl H., NAVAL MEDICAL RESEARCH INST BETHESDA MD, Siegel, Jeffrey N., and June, Carl H.
Abstract: T lymphocytes communicate with their environment through a large array of specialized cell surface receptors. These receptors provide signals which influence T cell ontogeny, activation by antigen, homing and many other aspects of T cell biology. Recent advances have provided a wealth of new information regarding the mechanism by which these surface receptors influence intracellular biochemical events. Transmembrane signaling is initiated by the binding of specific ligand to the extracellular portion of cell surface receptors. The signal is believed to be transmitted across the plasma membrane via either conformational change in the receptors, by receptor dimerization or by a change in its association with other proteins, Availability: Pub. in New Concepts in Immunodeficiency Diseases, p85-129 1993.
Published: 1993

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