Now showing items 1-18 of 18

    • Aquarium microbiome response to ninety-percent system water change : clues to microbiome management 

      Van Bonn, William; LaPointe, Allen; Gibbons, Sean M.; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (2015-04)
      The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the ...
    • Ecological succession and viability of human-associated microbiota on restroom surfaces 

      Gibbons, Sean M.; Schwartz, Tara; Fouquier, Jennifer; Mitchell, Michelle; Sangwan, Naseer; Gilbert, Jack A.; Kelley, Scott T. (2014-11-08)
      Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in 4 public restrooms, in situ bacterial communities were characterized hourly, daily, ...
    • The Genomic Standards Consortium 

      Field, Dawn; Amaral-Zettler, Linda A.; Cochrane, Guy R.; Cole, James R.; Dawyndt, Peter; Garrity, George M.; Gilbert, Jack A.; Glockner, Frank Oliver; Hirschman, Lynette; Karsch-Mizrachi, Ilene; Klenk, Hans-Peter; Knight, Rob; Kottmann, Renzo; Kyrpides, Nikos C.; Meyer, Folker; San Gil, Inigo; Sansone, Susanna-Assunta; Schriml, Lynn M.; Sterk, Peter; Tatusova, Tatiana; Ussery, David W.; White, Owen; Wooley, John (Public Library of Science, 2011-06-21)
      A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major ...
    • The genomic standards consortium : bringing standards to life for microbial ecology 

      Yilmaz, Pelin; Gilbert, Jack A.; Knight, Rob; Amaral-Zettler, Linda A.; Karsch-Mizrachi, Ilene; Cochrane, Guy R.; Nakamura, Yasukazu; Sansone, Susanna-Assunta; Glockner, Frank Oliver; Field, Dawn (Nature Publishing Group, 2011-04-07)
      Interest in sampling of diverse environments, combined with advances in high-throughput sequencing, vastly accelerates the pace at which new genomes and metagenomes are generated. For example, as of January 2011, 12 ...
    • Genomic Standards Consortium projects 

      Field, Dawn; Sterk, Peter; Kottmann, Renzo; De Smet, Wim; Amaral-Zettler, Linda A.; Cochrane, Guy R.; James, Cole R.; Davies, Neil; Dawyndt, Peter; Garrity, George M.; Gilbert, Jack A.; Glockner, Frank Oliver; Hirschman, Lynette; Klenk, Hans-Peter; Knight, Rob; Kyrpides, Nikos C.; Meyer, Folker; Karsch-Mizrachi, Ilene; Morrison, Norman; Robbins, Robert J.; San Gil, Inigo; Sansone, Susanna-Assunta; Schriml, Lynn M.; Tatusova, Tatiana; Ussery, David W.; Yilmaz, Pelin; White, Owen; Wooley, John; Caporaso, Gregory (Genomic Standards Consortium, 2014)
      The Genomic Standards Consortium (GSC) is an open-membership community working towards the development, implementation and harmonization of standards in the field of genomics. The mission of the GSC is to improve digital ...
    • Lifestyle evolution in cyanobacterial symbionts of sponges 

      Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M.; Haber, Markus; Blom, Jochen; Marshall, Christopher W.; Gilbert, Jack A.; Hentschel, Ute; Steindler, Laura (American Society for Microbiology, 2015-06-02)
      The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The ...
    • Microbial diversity - exploration of natural ecosystems and microbiomes 

      Gibbons, Sean M.; Gilbert, Jack A. (2015-09-29)
      Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to ...
    • Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 

      Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R.; Amaral-Zettler, Linda A.; Gilbert, Jack A.; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy R.; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serra, Philippe; Sterk, Peter; Arumugam, Manimozhiyan; Bailey, Mark; Baumgartner, Laura; Birren, Bruce W.; Blaser, Martin J.; Bonazzi, Vivien; Booth, Tim; Bork, Peer; Bushman, Frederic D.; Buttigieg, Pier Luigi; Chain, Patrick S. G.; Charlson, Emily; Costello, Elizabeth K.; Huot-Creasy, Heather; Dawyndt, Peter; DeSantis, Todd; Fierer, Noah; Fuhrman, Jed A.; Gallery, Rachel E.; Gevers, Dirk; Gibbs, Richard A.; San Gil, Inigo; Gonzalez, Antonio; Gordon, Jeffrey I.; Guralnick, Robert P.; Hankeln, Wolfgang; Highlander, Sarah; Hugenholtz, Philip; Jansson, Janet K.; Kau, Andrew L.; Kelley, Scott T.; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos C.; Larsen, Robert; Lauber, Christian L.; Legg, Teresa; Ley, Ruth E.; Lozupone, Catherine A.; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methe, Barbara A.; Meyer, Folker; Muegge, Brian; Nakielny, Sara; Nelson, Karen E.; Nemergut, Diana; Neufeld, Josh D.; Newbold, Lindsay K.; Oliver, Anna E.; Pace, Norman R.; Palanisamy, Giriprakash; Peplies, Jorg; Petrosino, Joseph; Proctor, Lita; Pruesse, Elmar; Quast, Christian; Raes, Jeroen; Ratnasingham, Sujeevan; Ravel, Jacques; Relman, David A.; Assunta-Sansone, Susanna; Schloss, Patrick D.; Schriml, Lynn M.; Sinha, Rohini; Smith, Michelle I.; Sodergren, Erica; Spor, Ayme; Stombaugh, Jesse; Tiedje, James M.; Ward, Doyle V.; Weinstock, George M.; Wendel, Doug; White, Owen; Whiteley, Andrew; Wilke, Andreas; Wortman, Jennifer R.; Yatsunenko, Tanya; Glockner, Frank Oliver (2011-01-04)
      Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the ...
    • The obese gut microbiome across the epidemiologic transition 

      Dugas, Lara R.; Fuller, Miles; Gilbert, Jack A.; Layden, Brian T. (BioMed Central, 2016-01-11)
      The obesity epidemic has emerged over the past few decades and is thought to be a result of both genetic and environmental factors. A newly identified factor, the gut microbiota, which is a bacterial ecosystem residing ...
    • The ocean sampling day consortium 

      Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Georgios; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O’Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-Clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loscher, Carolin R.; Kremp, Anke; DeLorenzo, Marie E.; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; ten Hoopen, Petra; Cochrane, Guy; L’Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Herrera Silveira, Jorge A.; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Fronth Nyhus, Paul Anders; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J.; Amaral-Zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Glockner, Frank Oliver (BioMed Central, 2015-06-19)
      Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. ...
    • RCN4GSC Workshop Report : managing data at the interface of biodiversity and (meta)genomics, March 2011 

      Robbins, Robert J.; Amaral-Zettler, Linda A.; Bik, Holly; Blum, Stan D.; Edwards, James; Field, Dawn; Garrity, George M.; Gilbert, Jack A.; Kottmann, Renzo; Krishtalka, Leonard; Lapp, Hilmar; Lawrence, Carolyn; Morrison, Norman; O Tuama, Eamonn; Parr, Cynthia Sims; San Gil, Inigo; Schindel, David; Schriml, Lynn M.; Vieglas, David; Wooley, John (Genomic Standards Consortium, 2012-07-28)
      Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify ...
    • Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012 

      Davies, Neil; Field, Dawn; Amaral-Zettler, Linda A.; Bicak, Mesude; Bourlat, Sarah; Coddington, Jonathan; Deck, John; Drummond, Alexei; Gilbert, Jack A.; Glockner, Frank Oliver; Kottmann, Renzo; Meyer, Chris; Morrison, Norman; Obst, Matthias; Robbins, Robert J.; Schriml, Lynn M.; Sterk, Peter; Stones-Havas, Steven (Genomic Standards Consortium, 2014)
      This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The workshop’s primary goal was to work towards the launch of the ...
    • Satellite remote sensing data can be used to model marine microbial metabolite turnover 

      Larsen, Peter E.; Scott, Nicole; Post, Anton F.; Field, Dawn; Knight, Rob; Hamada, Yuki; Gilbert, Jack A. (Nature Publishing Group, 2014-07-29)
      Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial ...
    • The seasonal structure of microbial communities in the Western English Channel 

      Gilbert, Jack A.; Field, Dawn; Swift, Paul; Newbold, Lindsay K.; Oliver, Anna E.; Smyth, Tim J.; Somerfield, Paul J.; Huse, Susan M.; Joint, Ian (2009-06-05)
      Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community ...
    • A simple novel device for air sampling by electrokinetic capture 

      Gordon, Julian; Gandhi, Prasanthi; Shekhawat, Gajendra; Frazier, Angel; Hampton-Marcell, Jarrad T.; Gilbert, Jack A. (BioMed Central, 2015-12-27)
      A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use ...
    • The taxonomic and functional diversity of microbes at a temperate coastal site : a ‘multi-omic’ study of seasonal and diel temporal variation 

      Gilbert, Jack A.; Field, Dawn; Swift, Paul; Thomas, Simon; Cummings, Denise; Temperton, Ben; Weynberg, Karen; Huse, Susan M.; Hughes, Margaret; Joint, Ian; Somerfield, Paul J.; Muhling, Martin (Public Library of Science, 2010-11-29)
      How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure ...
    • Toward interoperable bioscience data 

      Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral-Zettler, Linda A.; Begley, Kimberly; Booth, Tim; Bougueleret, Lydie; Burns, Gully; Chapman, Brad; Clark, Tim; Coleman, Lee-Ann; Copeland, Jay; Das, Sudeshna; de Daruvar, Antoine; de Matos, Paula; Dix, Ian; Edmunds, Scott; Evelo, Chris T.; Forster, Mark K.; Gaudet, Pascale; Gilbert, Jack A.; Goble, Carole; Griffin, Julian L.; Jacob, Daniel; Kleinjans, Jos; Harland, Lee; Haug, Kenneth; Hermjakob, Henning; Ho Sui, Shannan J.; Laederach, Alain; Liang, Shaoguang; Marshall, Stephen; McGrath, Annette; Merrill, Emily; Reilly, Dorothy; Roux, Magali; Shamu, Caroline E.; Shang, Catherine A.; Steinbeck, Christoph; Trefethen, Anne; Williams-Jones, Bryn; Wolstencroft, Katherine; Xenarios, Ioannis; Hide, Winston (Nature Publishing Group, 2012-01-27)
      To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the ...