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1. A framework for human microbiome research

Author

Rosamond Rhodes, Asif T. Chinwalla, Tessa Madden, Ashlee M. Earl, Maria C. Rivera, Candace N. Farmer, Jonathan M. Goldberg, Karthik Kota, Victor Felix, Nicholas B. King, Shibu Yooseph, Erica Sodergren, Monika Bihan, Martin J. Blaser, Dirk Gevers, Dan Knights, Pamela Sankar, Anup Mahurkar, Heather Huot Creasy, Veena Bhonagiri, Thomas M. Schmidt, Curtis Huttenhower, Mina Rho, Todd J. Treangen, Thomas J. Sharpton, I. Min A. Chen, Bo Liu, Sarah K. Highlander, Catherine C. Davis, Susan M. Huse, Richard A. Gibbs, Noam J. Davidovics, Patricio S. La Rosa, Carsten Russ, Wesley C. Warren, Richard K. Wilson, Patrick Minx, Jean E. McEwen, Alyxandria M. Schubert, Scott Anderson, Bonnie P. Youmans, Jamison McCorrison, Kathie A. Mihindukulasuriya, Vandita Joshi, Peter J. Mannon, Brandi L. Cantarel, Joseph F. Petrosino, Jack D. Sobel, Chandri Yandava, Sharvari Gujja, Janet K. Jansson, David J. Dooling, Daniel McDonald, Rob Knight, Granger G. Sutton, Gary C. Armitage, Larry J. Forney, Robert S. Fulton, Yuan Qing Wu, Jonathan Crabtree, Susan Kinder-Haake, Lu Wang, Liang Ye, Victor M. Markowitz, Narmada Shenoy, Elizabeth A. Lobos, Ruth M. Farrell, Tatiana A. Vishnivetskaya, Patrick S. G. Chain, Jacques Ravel, Katherine H. Huang, Sergey Koren, Yan Ding, Christina Giblin, Jason R. Miller, Michelle G. Giglio, Gina A. Simone, Chad Nusbaum, Lynn M. Schriml, Matthew C. Ross, Daniel D. Sommer, Sandra L. Lee, Theresa A. Hepburn, Michael Holder, Shaila Chhibba, Patrick D. Schloss, Omry Koren, Lan Zhang, Catrina Fronick, Richard R. Sharp, Diana Tabbaa, Yuzhen Ye, Dennis C. Friedrich, Christie Kovar, Owen White, A. Scott Durkin, Michael Feldgarden, Gary L. Andersen, Makedonka Mitreva, Todd Wylie, Nihar U. Sheth, Sheila Fisher, John Martin, Jose C. Clemente, Xiang Qin, James Versalovic, Dana A. Busam, Bruce W. Birren, Jeremy Zucker, Yu-Hui Rogers, Shannon Dugan, Kristine M. Wylie, Katherine P. Lemon, Floyd E. Dewhirst, Nicola Segata, Konstantinos Liolios, Anthony A. Fodor, Elizabeth L. Appelbaum, Ramana Madupu, W. Michael Dunne, Katherine S. Pollard, Leslie Foster, Olukemi O. Abolude, Yue Liu, Nikos C. Kyrpides, Christopher Wellington, Yanjiao Zhou, Lita M. Proctor, Tsegahiwot Belachew, Mircea Podar, Julia A. Segre, Holli A. Hamilton, Aye Wollam, Paul Spicer, Lei Chen, Sarah Young, Beltran Rodriguez-Mueller, Todd Z. DeSantis, Sean M. Sykes, Toby Bloom, Kelvin Li, Shane Canon, Catherine Jordan, Manolito Torralba, Brandi Herter, R. Dwayne Lunsford, Krishna Palaniappan, Jeroen Raes, Hongyu Gao, Barbara A. Methé, Kjersti Aagaard, Amy L. McGuire, Jonathan Friedman, Matthew D. Pearson, Jason Walker, Mary A. Cutting, Jonathan H. Badger, Diane E. Hoffmann, Tulin Ayvaz, Michael Fitzgerald, Brian J. Haas, Ravi Sanka, Doyle V. Ward, Kris A. Wetterstrand, Mark A. Watson, Christopher Smillie, Lucinda Fulton, Zhengyuan Wang, Lisa Begg, James R. White, Konstantinos Mavrommatis, Lucia Alvarado, Pamela McInnes, Emily L. Harris, Harindra Arachchi, Craig Pohl, Catherine A. Lozupone, Ruth E. Ley, Clinton Howarth, Yiming Zhu, Huaiyang Jiang, Gregory A. Buck, Carl C. Baker, Kimberley D. Delehaunty, Cristyn Kells, Katarzyna Wilczek-Boney, Kim C. Worley, Cesar Arze, J. Fah Sathirapongsasuti, Carolyn Deal, Sandra W. Clifton, Ken Chu, Rachel L. Erlich, Elaine R. Mardis, Cecil M. Lewis, Niall Lennon, Margaret Priest, Scott T. Kelley, Kymberlie Hallsworth-Pepin, Jane Peterson, Allison D. Griggs, Michelle O'Laughlin, Heidi H. Kong, Joshua Orvis, Maria Y. Giovanni, Sahar Abubucker, Dawn Ciulla, Sean Conlan, Chien Chi Lo, Antonio Gonzalez, Georgia Giannoukos, Jennifer R. Wortman, Paul Brooks, Jacques Izard, Chad Tomlinson, Donna M. Muzny, Shital M. Patel, Eric J. Alm, George M. Weinstock, Irene Newsham, Jeffrey G. Reid, Karoline Faust, Qiandong Zeng, Elena Deych, Nathalia Garcia, Mathangi Thiagarajan, James A. Katancik, Vivien Bonazzi, Robert C. Edgar, Christian J. Buhay, Indresh Singh, Johannes B. Goll, Ioanna Pagani, Vincent Magrini, Wendy A. Keitel, Emma Allen-Vercoe, Teena Mehta, Jeffery A. Schloss, William D. Shannon, Mihai Pop, Matthew B. Scholz, Valentina Di Francesco, Rebecca Truty, Karen E. Nelson, Kevin Riehle, Lora Lewis, Joseph L. Campbell, Laurie Zoloth, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Friedman, Jonathan, Smillie, Chris Scott, and Alm, Eric J.

Subjects
Adult, Male, Adolescent, Statistics as Topic, Population, Computational biology, Biology, Genome, Article, Young Adult, 03 medical and health sciences, Human health, 0302 clinical medicine, RNA, Ribosomal, 16S, Humans, Microbiome, education, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Bacteria, Human microbiome, Reference Standards, Metagenomics, 030220 oncology & carcinogenesis, Earth Microbiome Project, Metagenome, Female, Human Microbiome Project
Abstract

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Published
2012

2. High quality draft genome sequence of Segniliparus rugosus CDC 945T= (ATCC BAA-974T)

Author

Christopher A. Desjardins, Michael Fitzgerald, Ashlee M. Earl, Teena Mehta, Bruce W. Birren, Qiandong Zeng, Nadege C. Toney, James E. Posey, Janice Carr, Allison D. Griggs, W. Ray Butler, and Harindra Arachchi

Subjects
Whole genome sequencing, Genetics, 0303 health sciences, Human Microbiome Project, Rugosus, 030306 microbiology, Segniliparaceae,genome sequencing, RNA, Biology, biology.organism_classification, Genome, DNA sequencing, Short Genome Reports, 3. Good health, 03 medical and health sciences, Genus, Gene, 030304 developmental biology
Abstract

Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon-chain length mycolic acids bound in the cell wall. S. rugosus is also a medically important species because it is an opportunistic pathogen associated with mammalian lung disease. This report represents the second species in the genus to have its genome sequenced. The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part of the NIH Roadmap for Medical Research, Human Microbiome Project.

Published
2011
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3. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Frances Letendre, Vasilia Magnisalis, Helen Vassiliev, Rebecca Reyes, Maura Costello, St Christophe Acer, Pen MacDonald, Geneva Young, Katherine Thompson, Iain MacCallum, Tarjei S. Mikkelsen, Andy Vo, Eva Markiewicz, Yeshi Lokyitsang, Sharon Stavropoulos, Rachel Mittelman, Xiaohui Xie, Diallo Ferguson, James Cuff, Terence P. Speed, Catherine Stone, Tanya Mihova, Janine E. Deakin, Aaron M. Berlin, David A. Ray, David D. Pollock, Ben Kanga, Kunsang Gyaltsen, Scott Anderson, Gary Gearin, Nabil Hafez, Lisa Chuda, Marco A. Marra, David B. Jaffe, Leonid Boguslavskiy, Asha Kamat, Jonathan Butler, Alicia Franke, Lynne Aftuck, Sheridon Channer, Rosie Levine, Kerstin Lindblad-Toh, Birhane Hagos, Imane Bourzgui, Monika D. Huard, Tamrat Negash, Jamal Abdulkadir, Tsering Wangchuk, Georgius De Haan, Sheila Fisher, Justin Abreu, Abderrahim Farina, Kebede Maru, M. Erii Husby, Peter Kisner, Kunsang Dorjee, Jacob L. Glass, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Christina R. Gearin, Otero L. Oyono, Atanas Mihalev, Yama Thoulutsang, Katie D'Aco, Choe Norbu, Christopher Strader, Edda Koina, Allen Alexander, Barry O'Neill, William Brockman, Wanjun Gu, Richard Elong, Keenan Ross, Shailendra Yadav, Alan Dupes, Seva Kashin, James Meldrim, Dmitry Khazanovich, Passang Dorje, Adal Abebe, April Cook, Matthew Breen, Randy L. Jirtle, Shangtao Liu, Jean L. Chang, Patrick Cahill, Claire M. Wade, Chee Whye Chin, Dennis C. Friedrich, Tina Goode, Cecil Rise, Robert D. Nicholls, Peter Rogov, Adam Brown, Oana Mihai, Sujaa Raghuraman, Adam Wilson, Marcia Lara, Chelsea D. Foley, Susan Faro, Sampath Settipalli, Thu Nguyen, Matthew Wakefield, Xiaohong Liu, Anna Montmayeur, Jerzy Jurka, Ngawang Sherpa, Riza M. Daza, Evan Mauceli, Senait Tesfaye, Sharleen Grewal, Susan McDonough, Leo Goodstadt, Manuel Garber, John M. Greally, Valentine Mlenga, Manfred Grabherr, Charles Matthews, Andrew Zimmer, Teena Mehta, Harindra Arachi, Mark A. Batzer, Rakela Lubonja, Margaret Priest, Diana Shih, Joseph Graham, Panayiotis V. Benos, Lance S. Davidow, Alex Lipovsky, Stephen M. J. Searle, Andreas Heger, Timothy A. Hore, Patrick Cooke, Leonidas Mulrain, Tsering Wangdi, Jennifer A. Marshall Graves, Sante Gnerre, Michelle L. Baker, Jacqueline E. Schein, Michael Weiand, Jessica Spaulding, Charlotte Henson, Jane Wilkinson, Terry Shea, Shannon E. Duke, William McCusker, Kerri Topham, Jerome Naylor, Lu Shi, Fritz Pierre, Claude Bonnet, Shaun Mahony, Michele Clamp, Katherine Belov, John L. VandeBerg, Nicole Stange-Thomann, Annie Lui, Radhika Das, Pema Phunkhang, Andrew J. Gentles, Elizabeth P. Ryan, Erica Anderson, Jill Falk, Bronwen Aken, Robert Nicol, Ted Sharpe, Sahal Osman, Missole Doricent, Michael Kleber, Jeannie T. Lee, Paul D. Waters, Melissa Fazzari, Jinlei Liu, Loryn Gadbois, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi, Caleb Webber, Tashi Bayul, Brikti Abera, Mayumi Oda, Gavin A. Huttley, Jennifer L. Hall, Chris P. Ponting, Michael Kamal, Kimberly Dooley, Mieke Citroen, Tsamla Tsamla, Ira Topping, Eric S. Lander, Edward Grandbois, Christopher Patti, Louis Meneus, Tracey Honan, Zuly E. Parra, Nga Nguyen, Todd Sparrow, Dawa Thoulutsang, Leanne Hughes, Yama Cheshatsang, Qing Yu, Niall J. Lennon, Nathaniel Novod, Christina Demaso, Anthony T. Papenfuss, Paul B. Samollow, Toby Bloom, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Zac Zwirko, Georgia Giannoukos, Michael C. Zody, Danni Zhong, Jason Blye, Stuart DeGray, Marc Azer, Robert D. Miller, Amr Abdouelleil, Brian Hurhula, Filip Rege, John Stalker, Andrew Barry, Pablo Alvarez, Norbu Dhargay, Krista Lance, Chris T. Amemiya, Jerilyn A. Walker, Jennifer R. Weidman, Peter An, Erin E. Dooley, William Lee, and Alville Collymore

Subjects
Genetics, Base Composition, Genome evolution, Genome, Multidisciplinary, Genomics, Opossums, Biology, biology.organism_classification, Polymorphism, Single Nucleotide, Synteny, Monodelphis domestica, Evolution, Molecular, X Chromosome Inactivation, Opossum, Molecular evolution, Protein Biosynthesis, DNA Transposable Elements, Animals, Humans, Gene family, Gene conversion, Conserved Sequence
Abstract

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Published
2007
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4. Extracellular electron transfer via microbial nanowires

Author

Kevin D. McCarthy, Gemma Reguera, Teena Mehta, Derek R. Lovley, Julie S. Nicoll, and Mark T. Tuominen

Subjects
Nanotechnology, Microscopy, Atomic Force, Ferric Compounds, Electron Transport, Exoelectrogen, Electron transfer, Microscopy, Electron, Transmission, Bacterial nanowires, Geobacter sulfurreducens, Phylogeny, chemistry.chemical_classification, Multidisciplinary, biology, Chemistry, Electric Conductivity, Geobacter metallireducens, Electron acceptor, biology.organism_classification, Electron transport chain, Nanostructures, Chemical engineering, Genes, Bacterial, Fimbriae, Bacterial, Mutation, Fimbriae Proteins, Geobacter, Biotechnology
Abstract

Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(iii) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments. Previous investigations on electron transfer to Fe(iii) have focused on the role of outer-membrane c-type cytochromes. However, some Fe(iii) reducers lack c-cytochromes. Geobacter species, which are the predominant Fe(iii) reducers in many environments, must directly contact Fe(iii) oxides to reduce them, and produce monolateral pili that were proposed, on the basis of the role of pili in other organisms, to aid in establishing contact with the Fe(iii) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(iii) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(iii) oxides. Electron transfer through pili indicates possibilities for other unique cell-surface and cell-cell interactions, and for bioengineering of novel conductive materials.

Published
2005
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5. Structure, function and diversity of the healthy human microbiome

Author

Catherine A. Lozupone, Paul Spicer, Margaret Priest, Todd J. Treangen, Niall J. Lennon, Thomas M. Schmidt, Sandra W. Clifton, Ken Chu, Vandita Joshi, Catherine C. Davis, Omry Koren, Yuanqing Wu, Christie Kovar, Jonathan Friedman, Matthew D. Pearson, Scott T. Kelley, Brandi L. Cantarel, Patrick S. G. Chain, Chad Nusbaum, Jonathan Crabtree, Lu Wang, Bonnie P. Youmans, James A. Katancik, George M. Weinstock, Granger G. Sutton, Lisa Begg, Candace N. Farmer, Victor Felix, Barbara A. Methé, Elena Deych, Martin J. Blaser, Amy L. McGuire, Pamela McInnes, Xiang Qin, James Versalovic, James R. White, Yan Ding, Christian J. Buhay, Jason R. Miller, Susan M. Huse, Wm. Michael Dunne, Vivien Bonazzi, Jeremy Zucker, Ioanna Pagani, Robert C. Edgar, Dana A. Busam, Gina A. Simone, Michael Feldgarden, Vincent Magrini, Richard A. Gibbs, Noam J. Davidovics, Indresh Singh, Lucinda Fulton, Lucia Alvarado, Rob Knight, Emma Allen-Vercoe, Teena Mehta, Patricio S. La Rosa, Carsten Russ, Joshua Orvis, Sahar Abubucker, Jacques Ravel, Richard R. Sharp, Dirk Gevers, Wesley C. Warren, Pamela Sankar, Chad Tomlinson, Donna M. Muzny, Jean E. McEwen, Nihar U. Sheth, Sheila Fisher, Katherine H. Huang, Dennis C. Friedrich, Gary C. Armitage, John Martin, Richard K. Wilson, Katarzyna Wilczek-Boney, Catrina Fronick, Patrick Minx, Rebecca Truty, William D. Shannon, Matthew B. Scholz, Kris A. Wetterstrand, Maria Y. Giovanni, Katherine P. Lemon, Floyd E. Dewhirst, Shaila Chhibba, Anthony A. Fodor, Lan Zhang, Patrick D. Schloss, Lynn M. Schriml, Doyle V. Ward, Diana Tabbaa, Jose C. Clemente, Larry J. Forney, Kimberley D. Delehaunty, Cesar Arze, Sharvari Gujja, Lita M. Proctor, Christopher Smillie, Elizabeth L. Appelbaum, Konstantinos Liolios, Chandri Yandava, David J. Dooling, Emily L. Harris, Katherine S. Pollard, Clinton Howarth, Tatiana A. Vishnivetskaya, Sarah Young, Huaiyang Jiang, Karoline Faust, Janet K. Jansson, Kymberlie Hallsworth-Pepin, Owen White, Thomas J. Sharpton, Yiming Zhu, Yanjiao Zhou, Julia A. Segre, Jason Walker, Heidi H. Kong, Toby Bloom, Mathangi Thiagarajan, Tulin Ayvaz, I. Min A. Chen, Bo Liu, Kim C. Worley, Jennifer R. Wortman, Susan Kinder Haake, Manolito Torralba, Makedonka Mitreva, Kjersti Aagaard, J. Fah Sathirapongsasuti, Carolyn Deal, Jeroen Raes, Olukemi O. Abolude, Yue Liu, Rachel L. Erlich, Gary L. Andersen, Nicola Segata, Christopher Wellington, Todd Wylie, Kristine M. Wylie, Tsegahiwot Belachew, Jonathan H. Badger, Mark A. Watson, Aye Wollam, Zhengyuan Wang, Michelle G. Giglio, Kelvin Li, Diane E. Hoffmann, Cristyn Kells, Daniel D. Sommer, Victor M. Markowitz, Chien Chi Lo, Karen E. Nelson, Brian J. Haas, Ruth M. Farrell, Craig Pohl, Harindra Arachchi, Nicholas B. King, Gregory A. Buck, Konstantinos Mavromatis, Qiandong Zeng, Krishna Palaniappan, Kathie A. Mihindukulasuriya, Dan Knights, Anup Mahurkar, Nathalia Garcia, Mary A. Cutting, Theresa A. Hepburn, Mina Rho, Catherine Jordan, Christina Giblin, Dawn Ciulla, Shital M. Patel, Eric J. Alm, Kevin Riehle, Irene Newsham, Sarah K. Highlander, Jamison McCorrison, Nikos C. Kyrpides, Mircea Podar, Beltran Rodriguez-Mueller, Lora Lewis, Robert S. Fulton, Yuzhen Ye, Joseph L. Campbell, Laurie Zoloth, R. Dwayne Lunsford, Ramana Madupu, A. Scott Durkin, Maria C. Rivera, Sergey Koren, Shibu Yooseph, Ruth E. Ley, Erica Sodergren, Cecil M. Lewis, Heather Huot Creasy, Joseph F. Petrosino, Jacques Izard, Jack D. Sobel, J. Paul Brooks, Jeffrey G. Reid, Antonio Gonzalez, Narmada Shenoy, Elizabeth A. Lobos, Georgia Giannoukos, Matthew C. Ross, Allison D. Griggs, Yu-Hui Rogers, Leslie Foster, Wendy A. Keitel, Lei Chen, Alyxandria M. Schubert, Scott Anderson, Peter J. Mannon, Shane Canon, Hongyu Gao, Mihai Pop, Holli A. Hamilton, Tessa Madden, Michelle Oglaughlin, Karthik Kota, Monika Bihan, Veena Bhonagiri, Michael Holder, Daniel McDonald, Liang Ye, Sandra L. Lee, Rosamond Rhodes, Asif T. Chinwalla, Ashlee M. Earl, Shannon Dugan, Sean Conlan, Johannes B. Goll, Jonathan M. Goldberg, Valentina Di Francesco, Curtis Huttenhower, Brandi Herter, Todd Z. DeSantis, Sean M. Sykes, Michael Fitzgerald, Elaine R. Mardis, Jane Peterson, Bruce W. Birren, Ravi Sanka, Carl C. Baker, Jeffery A. Schloss, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Alm, Eric J., Friedman, Jonathan, and Smillie, Christopher S.

Subjects
Adult, Male, Adolescent, Ecology (disciplines), Biology, Bioinformatics, 03 medical and health sciences, Young Adult, RNA, Ribosomal, 16S, Humans, Microbiome, Ecosystem, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Bacteria, 030306 microbiology, Gastrointestinal Microbiome, Human microbiome, Biodiversity, Phenotype, Evolutionary biology, Health, Earth Microbiome Project, Metagenome, Enterotype, Female, Oral Microbiome, Metagenomics, Metabolic Networks and Pathways, Human Microbiome Project
Abstract

Author Manuscript date: 2013 February 05., Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Published
2012

6. A catalog of reference genomes from the human microbiome

Author

Dirk Gevers, Doyle V. Ward, Sean M. Sykes, Justin Johnson, Michael Fitzgerald, Jessica B. Hostetler, Sarah Young, Dianhui Zhu, Jason R. Miller, Chinnappa D. Kodira, Aaron M. Berlin, Erica Sodergren, Michael G. Surette, Matthew D. Pearson, Asif T. Chinwalla, Ashlee M. Earl, Michael Feldgarden, Kim C. Worley, Christian J. Buhay, Lisa Hemphill, Manolito Torralba, Xiang Qin, Jonathan H. Badger, Clint Howarth, Marcus Gillis, Candace N. Farmer, Karen E. Nelson, Bruce W. Birren, Richard A. Gibbs, Sandra W. Clifton, Mike Holder, Aye Wollam, Carsten Russ, Wesley C. Warren, Brian J. Haas, Michelle G. Giglio, Qiang Xu, Richard K. Wilson, Patrick Minx, Scott Durkin, Chad Nusbaum, Craig Pohl, Robert S. Fulton, Steve Ferriera, Chandri N. Yandava, Sharvari Gujja, Qiandong Zeng, Ramana Madupu, Victor Markowitz, Joshua Orvis, Andrew Cree, Chad Tomlinson, Donna M. Muzny, Vandita Joshi, Amrita Pati, Christie Kovar, Theresa A. Hepburn, Nikos C. Kyrpides, Kymberlie H. Pepin, Douglas B. Rusch, Granger G. Sutton, Amr Abouellleil, Konstantinos Liolios, Sarah K. Highlander, Yan Ding, Jamison McCorrison, George M. Weinstock, Kris A. Wetterstrand, Emma Allen-Vercoe, Teena Mehta, Lucinda Fulton, Katarzyna Wilczek-Boney, Makedonka Mitreva, Lei Chen, Joseph F. Petrosino, Heather Huot Creasy, Shannon Dugan, Lan Zhang, Owen White, Robert L. Strausberg, Jennifer R. Wortman, Jonathan Crabtree, and Barbara A. Methé

Subjects
Sequence analysis, Respiratory System, Urogenital System, Biology, Genome, Article, Bacterial Proteins, Phylogenetics, Genome, Archaeal, Databases, Genetic, Humans, Microbiome, Gene, Phylogeny, Skin, Genetics, Mouth, Multidisciplinary, Bacteria, Human microbiome, Computational Biology, Genetic Variation, Biodiversity, Sequence Analysis, DNA, Gastrointestinal Tract, Metagenomics, Genes, Bacterial, Metagenome, Peptides, Genome, Bacterial, Reference genome
Abstract

The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

Published
2010

7. Evolution of genes and genomes on the Drosophila phylogeny

Author

Adam M. Phillippy, Edward Grandbois, Pen MacDonald, Iain MacCallum, Laura K. Reed, Wojciech Makalowski, Tracey Honan, Tania Tassinari Rieger, Melissa J. Hubisz, Josep M. Comeron, Douglas Smith, Jennifer Godfrey, Sebastian Strempel, Amr Abdouelleil, Brenton Gravely, Harindra Arachi, Albert J. Vilella, Marc Azer, Sarah A. Teichmann, Roger A. Hoskins, Corbin D. Jones, Keenan Ross, Derek Wilson, Stuart J. Newfeld, John Stalker, Thomas D. Watts, Dennis C. Friedrich, Therese A. Markow, Michael U. Mollenhauer, Tina Goode, Geneva Young, Terry Shea, Krista Lance, Karin A. Remington, Kevin A. Edwards, Lynne Aftuck, Cecil Rise, Sheridon Channer, Matthew D. Rasmussen, Nicole Stange-Thomann, Annie Lui, Robert A. Reenan, Todd Sparrow, Dave Begun, Tamrat Negash, Laura K. Sirot, Adrianne Brand, Adam Brown, Daisuke Yamamoto, Pema Phunkhang, Justin Abreu, Russell Schwartz, Ana Llopart, Abderrahim Farina, Kebede Maru, Chung-I Wu, Allen Alexander, Scott Anderson, So Jeong Lee, Jason Blye, Gary H. Karpen, Wilfried Haerty, Daniel A. Barbash, Peter Rogov, Barry O'Neill, Rachel Mittelman, Jakob Skou Pedersen, Leanne Hughes, Robert K. Bradley, Graziano Pesole, Wyatt W. Anderson, Anthony J. Greenberg, Alejandro Sánchez-Gracia, Julio Rozas, Stephen W. Schaeffer, Yama Thoulutsang, Roger K. Butlin, David H. Ardell, Stuart DeGray, Chris P. Ponting, Deborah E. Stage, Corrado Caggese, Montserrat Aguadé, Casey M. Bergman, Diallo Ferguson, Peili Zhang, Jeffrey R. Powell, Hajime Sato, Xiaohong Liu, Marta Sabariego Puig, Michael Parisi, Passang Dorje, Yoshihiko Tomimura, Adal Abebe, Carlo G. Artieri, Brian Hurhula, Filip Rege, Peter D. Keightley, Andrew Barry, Pablo Alvarez, Tsamla Tsamla, Marvin Wasserman, Santosh Jagadeeshan, Daniel L. Halligan, Chelsea D. Foley, Kim D. Delehaunty, Manfred Grabherr, Sourav Chatterji, Angela N. Brooks, James C. Costello, Mieke Citroen, James A. Yorke, Hsiao Pei Yang, Charles Chapple, Jian Lu, Carlos A. Machado, Norbu Dhargay, Tsering Wangchuk, Anat Caspi, Patrick Cahill, Tashi Bayul, Lisa Levesque, Otero L. Oyono, Atanas Mihalev, Dawa Thoulutsang, Dawn N. Abt, Sujaa Raghuraman, Manyuan Long, Maria Mendez-Lago, Charles Matthews, Kimberly Dooley, Alex Wong, Melanie A. Huntley, William R. Jeck, Ira Topping, Ben Kanga, José P. Abad, Ana Cristina Lauer Garcia, Brikti Abera, Kunsang Gyaltsen, Jonathan Butler, Alicia Franke, Michael C. Schatz, Cheewhye Chin, Charles F. Aquadro, Justin Johnson, Bryant F. McAllister, Georgia Giannoukos, M. Erii Husby, Rod A. Wing, Shangtao Liu, Jean L. Chang, Jennifer Daub, Eiko Kataoka, Leopold Parts, Rakela Lubonja, Margaret Priest, Yoshiko N. Tobari, Teena Mehta, Evgeny M. Zdobnov, Yeshi Lokyitsang, Richard Elong, Matthew J. Parisi, Louis Meneus, Eric S. Lander, Alan Filipski, Gary Gearin, Nabil Hafez, Nicholas Sisneros, David B. Jaffe, Ian Holmes, Marina Sirota, Leonid Boguslavskiy, Lisa Chuda, LaDeana W. Hillier, Meizhong Luo, Phil Batterham, Michael Kleber, Richard K. Wilson, Yama Cheshatsang, Qing Yu, Rebecca Reyes, Matthew W. Hahn, Andreas Heger, Mar Marzo, Patrick Minx, Kerstin Lindblad-Toh, Vera L. S. Valente, Adam Wilson, William C. Jordan, Mohamed A. F. Noor, Chiao-Feng Lin, Asha Kamat, Heather Ebling, Mihai Pop, Frances Letendre, Mariana F. Wolfner, Don Gilbert, Ngawang Sherpa, Riza M. Daza, Oana Mihai, Gabriel C. Wu, Aaron M. Berlin, Ewen F. Kirkness, Monika D. Huard, Robert S. Fulton, Randall H. Brown, Danni Zhong, Sharon Stavropoulos, Venky N. Iyer, Xu Mu, Christina R. Gearin, David M. Rand, Jerry A. Coyne, Dan Hultmark, Jill Falk, Christopher Patti, Montserrat Papaceit, James Meldrim, Valentine Mlenga, Muneo Matsuda, Sven Findeiß, Todd A. Schlenke, Kevin McKernan, Brian P. Walenz, Timothy B. Sackton, Leonardo Koerich, Peter An, Robert Nicol, Chuong B. Do, Dmitry Khazanovich, Carmen Segarra, Maura Costello, St Christophe Acer, Claudia Rohde, Serafim Batzoglou, Hadi Quesneville, Evan Mauceli, Andy Vo, Luciano M. Matzkin, Susan E. Celniker, Patrick M. O’Grady, William M. Gelbart, Lloyd Low, Jamal Abdulkadir, Jessica Spaulding, Brian R. Calvi, Charlotte Henson, Robert David, Jennifer L. Hall, Andrew G. Clark, Anastasia Gardiner, Susan M. Russo, Birhane Hagos, Kerri Topham, Amy Denise Reily, Eli Venter, Jerome Naylor, Sandra W. Clifton, Valer Gotea, Samuel R. Gross, Manolis Kellis, Claude Bonnet, Christopher Strader, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Stephen M. Mount, Robert L. Strausberg, Shailendra Yadav, Kristipati Ravi Ram, Steven L. Salzberg, Erik Gustafson, David A. Garfield, Eva Freyhult, Arthur L. Delcher, Enrico Blanco, Granger G. Sutton, Jason M. Tsolas, Charles Robin, Angie S. Hinrichs, Christopher D. Smith, Jane Wilkinson, Brendan McKernan, Fritz Pierre, William McCusker, Brian Oliver, Barry E. Garvin, Sudhir Kumar, Peter Kisner, Kunsang Dorjee, A. Bernardo Carvalho, Anna Montmayeur, Andrew Zimmer, Diana Shih, Wei Tao, Shiaw Pyng Yang, Sante Gnerre, Sampath Settipalli, Thu Nguyen, Paolo Barsanti, Brian P. Lazzaro, Sonja J. Prohaska, J. Craig Venter, Senait Tesfaye, Susan McDonough, Kim D. Pruitt, Alexander Stark, Sergio Castrezana, Lucinda Fulton, Richard T. Lapoint, Greg Gibson, John Spieth, Boris Adryan, Georgius De Haan, Sheila Fisher, Daniel A. Pollard, Seva Kashin, Rob J. Kulathinal, Michael B. Eisen, Nathaniel Novod, Christina Demaso, Alan Dupes, Amanda M. Larracuente, Toby Bloom, Alfredo Villasante, Charles H. Langley, Rama S. Singh, Niall J. Lennon, Kristi L. Montooth, Daniel Barker, Wolfgang Stephan, David Sturgill, Ruiqiang Li, Andrew Hollinger, Boris Boukhgalter, Talene Thomson, Patrick Cooke, Zac Zwirko, Nadia D. Singh, Michael Weiand, Lior Pachter, Roderic Guigó, Yu Zhang, Jay D. Evans, Stephanie Bosak, Rosie Levine, Lu Shi, Kiyohito Yoshida, Carolyn S. McBride, Pouya Kheradpour, William Brockman, Alberto Civetta, Hiroshi Akashi, Marcia Lara, Susan Faro, Sam Griffiths-Jones, Michael R. Brent, Thomas H. Eickbush, Gane Ka-Shu Wong, Elizabeth P. Ryan, Erica Anderson, Roberta Kwok, Asif T. Chinwalla, Sahal Osman, Nga Nguyen, Damiano Porcelli, Missole Doricent, Saverio Vicario, Marc Rubenfield, Bárbara Negre, Gillian M. Halter, Erin E. Dooley, Elena R. Lozovsky, William Lee, Alville Collymore, Catherine Stone, Tanya Mihova, Jun Wang, Karsten Kristiansen, Imane Bourzgui, Michael F. Lin, Katie D'Aco, Filipe G. Vieira, Choe Norbu, Yu-Hui Rogers, Aaron L. Halpern, Eugene W. Myers, Sharleen Grewal, Robert T. Good, Alfredo Ruiz, Dave Kudrna, Joseph Graham, Alex Lipovsky, Leonidas Mulrain, Tsering Wangdi, Roman Arguello, Mira V. Han, Arjun Bhutkar, Rasmus Nielsen, David J. Saranga, Aleksey V. Zimin, Vasilia Magnisalis, Helen Vassiliev, Thomas C. Kaufman, Eva Markiewicz, Temple F. Smith, Jinlei Liu, Loryn Gadbois, Michael G. Ritchie, Lisa Zembek, Daniel Bessette, Pasang Bachantsang, Adam Navidi, Department of Molecular Biology and Genetics, Cornell University [New York], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of California [Berkeley], University of California, Agencourt Bioscience Corporation, Partenaires INRAE, Faculty of Life Science, University of Manchester [Manchester], Laboratory of Cellular and Developmental Biology (LCDB), NIDDK, NIH, Department of Ecology and Evolutionary Biology, University of Arizona, Department of Biology, Indiana University [Bloomington], Indiana University System-Indiana University System, Massachusetts Institute of Technology (MIT), Harvard University [Cambridge], Centro de Biología Molecular Severo Ochoa [Madrid] (CBMSO), Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Brown University, Laboratory of Molecular Biology, Medical Research Council, Departament de Genetica, Universitat de Barcelona (UB), Pennsylvania State University (Penn State), Penn State System-Penn State System, Department of Genetics, University of Georgia [USA], Uppsala University, Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), McMaster University, School of Biology, IE University, Università degli Studi di Bari Aldo Moro, University of Melbourne, Stanford University, University of California [Davis] (UC Davis), Boston University [Boston] (BU), Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Washington University in Saint Louis (WUSTL), University of Sheffield, Syracuse University, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Department of Bioengineering, Beihang University (BUAA), Tucson Stock Center, Genome Center, University of California-University of California, Genome Sequencing Center, University of Washington School of Medicine, University of Winnipeg, Iowa State University (ISU), Indiana University System, The Wellcome Trust Sanger Institute [Cambridge], Center for Bioinformatics and Computational Biology, University of Delaware [Newark], Illinois State University, University of Rochester [USA], United States Department of Agriculture (USDA), Arizona State University [Tempe] (ASU), Leipzig University, Universidade Federal do Rio Grande do Sul (UFRGS), Duke University, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of Connecticut (UCONN), Computer Science Département, Université Saint-Esprit de Kaslik (USEK), Mc Master University, Indiana University, Institute of Evolutionary Biology, University of Edinburgh, J. Craig Venter Institute [La Jolla, USA] (JCVI), University of Oxford [Oxford], Center for Biomolecular Science and Engineering, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), and Zdobnov, Evgeny

Subjects
melanogaster genome, 0106 biological sciences, RNA, Untranslated, [SDV]Life Sciences [q-bio], Genome, Insect, RNA, Untranslated/genetics, Genes, Insect, 01 natural sciences, Genome, Genome, Insect/ genetics, Gene Order, Genome, Mitochondrial/genetics, Drosophila Proteins, Phylogeny, ddc:616, Genetics, 0303 health sciences, Multidisciplinary, biology, Reproduction, Genomics, Multigene Family/genetics, Reproduction/genetics, DNA Transposable Elements/genetics, Genes, Insect/ genetics, Multigene Family, dosage compensation, Drosophila, amino-acid substitution, Drosophila Protein, Drosophila Proteins/genetics, Synteny/genetics, fruit-fly, 010603 evolutionary biology, Synteny, Drosophila sechellia, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Molecular evolution, Codon/genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, adaptive protein evolution, Codon, 030304 developmental biology, Gene Order/genetics, molecular evolution, fungi, Immunity, synonymous codon usage, Sequence Analysis, DNA, Immunity/genetics, biology.organism_classification, Drosophila mojavensis, Evolutionary biology, Genome, Mitochondrial, DNA Transposable Elements, maximum-likelihood, noncoding dna, Drosophila/ classification/ genetics/immunology/metabolism, Sequence Alignment, natural-selection, Drosophila yakuba
Abstract

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Published
2007
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8. Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens

Author

Trevor L. Woodard, Joy E. Ward, Dawn E. Holmes, Jennifer Webster, Anna Liu, Derek R. Lovley, Barbara A. Methé, Kelly P. Nevin, Teena Mehta, and Swades K. Chaudhuri

Subjects
Cytochrome, Microbiology, Transcriptome, Electron transfer, Gene expression, RNA, Messenger, Gene, Geobacter sulfurreducens, Electrodes, Ecology, Evolution, Behavior and Systematics, Oligonucleotide Array Sequence Analysis, biology, Reverse Transcriptase Polymerase Chain Reaction, Cytochromes c, Gene Expression Regulation, Bacterial, biology.organism_classification, Blotting, Northern, Reverse transcription polymerase chain reaction, Electrophysiology, RNA, Bacterial, Biochemistry, Pilin, biology.protein, Geobacter, Oxidation-Reduction, Bacterial Outer Membrane Proteins
Abstract

Summary Whole-genome analysis of gene expression in Geobacter sulfurreducens revealed 474 genes with transcript levels that were significantly different during growth with an electrode as the sole electron acceptor versus growth on Fe(III) citrate. The greatest response was a more than 19-fold increase in transcript levels for omcS , which encodes an outer-membrane cytochrome previously shown to be required for Fe(III) oxide reduction. Quantitative reverse transcription polymerase chain reaction and Northern analyses confirmed the higher levels of omcS transcripts, which increased as power production increased. Deletion of omcS inhibited current production that was restored when omcS was expressed in trans. Transcript expression and genetic analysis suggested that OmcE, another outer-membrane cytochrome, is also involved in electron transfer to electrodes. Surprisingly, genes for other proteins known to be important in Fe(III) reduction such as the outer-membrane c -type cytochrome, OmcB, and the electrically conductive pilin ‘nanowires’ did not have higher transcript levels on electrodes, and deletion of the relevant genes did not inhibit power production. Changes in the transcriptome suggested that cells growing on electrodes were subjected to less oxidative stress than cells growing on Fe(III) citrate and that a number of genes annotated as encoding metal efflux proteins or proteins of unknown function may be important for growth on electrodes. These results demonstrate for the first time that it is possible to evaluate gene expression, and hence the metabolic state, of microorganisms growing on electrodes on a genome-wide basis and suggest that OmcS, and to a lesser extent OmcE, are important in electron transfer to electrodes. This has important implications for the design of electrode materials and the genetic engineering of microorganisms to improve the function of microbial fuel cells.

Published
2006

9. A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens

Author

Richard H. Glaven, Derek R. Lovley, Teena Mehta, Tünde Mester, and Susan E. Childers

Subjects
Oxidase test, biology, Type II secretion system, Chemistry, Mutant, Oxides, Periplasmic space, Fibronectin type III domain, biology.organism_classification, Microbiology, Ferric Compounds, Electron Transport, Biochemistry, Manganese Compounds, Mutation, Fimbriae Proteins, Leptothrix discophora, Geobacter, Geobacter sulfurreducens, Oxidation-Reduction, Bacterial Outer Membrane Proteins
Abstract

Extracellular electron transfer onto Fe(III) oxides in Geobacter sulfurreducens is considered to require proteins that must be exported to the outer surface of the cell. In order to investigate this, the putative gene for OxpG, the pseudopilin involved in a type II general secretion pathway of Gram-negative bacteria, was deleted. The mutant was unable to grow with insoluble Fe(III) oxide as the electron acceptor. Growth on soluble Fe(III) was not affected. An analysis of proteins that accumulated in the periplasm of the oxpG mutant, but not in the wild-type, led to the identification of a secreted protein, OmpB. OmpB is predicted to be a multicopper protein, with highest homology to the manganese oxidase, MofA, from Leptothrix discophora. OmpB contains a potential Fe(III)-binding site and a fibronectin type III domain, suggesting a possible role for this protein in accessing Fe(III) oxides. OmpB was localized to the membrane fraction of G. sulfurreducens and in the supernatant of growing cultures, consistent with the type II secretion system exporting OmpB. A mutant in which ompB was deleted had the same phenotype as the oxpG mutant, suggesting that the failure to export OmpB was responsible for the inability of the oxpG-deficient mutant to reduce Fe(III) oxide. This is the first report that proposes a role for a multicopper oxidase-like protein in an anaerobic organism. These results further emphasize the importance of outer-membrane proteins in Fe(III) oxide reduction and suggest that outer-membrane proteins other than c-type cytochromes are required for Fe(III) oxide reduction in Geobacter species.

Published
2006

10. Outer Membrane c-Type Cytochromes Required for Fe(III) and Mn(IV) Oxide Reduction in Geobacter sulfurreducens

Author

Derek R. Lovley, Maddalena V. Coppi, Susan E. Childers, and Teena Mehta

Subjects
Cytochrome, Inorganic chemistry, Molecular Sequence Data, Oxide, Applied Microbiology and Biotechnology, Ferric Compounds, chemistry.chemical_compound, Electron transfer, Bacterial Proteins, Amino Acid Sequence, Geobacter sulfurreducens, DNA Primers, chemistry.chemical_classification, Ecology, biology, Base Sequence, Cytochrome c, Nitrilotriacetic acid, Cytochromes c, Oxides, Electron acceptor, biology.organism_classification, Physiology and Biotechnology, Peptide Fragments, Kinetics, chemistry, Manganese Compounds, biology.protein, Bacterial outer membrane, Geobacter, Oxidation-Reduction, Food Science, Biotechnology, Nuclear chemistry, Bacterial Outer Membrane Proteins
Abstract

The potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides by Geobacter sulfurreducens was investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the outer surfaces of intact cells were c -type cytochromes. One, designated OmcS, has a molecular mass of ca. 50 kDa and is predicted to be an outer membrane hexaheme c- type cytochrome. Transcripts for omcS could be detected during growth on Fe(III) oxide, but not on soluble Fe(III) citrate. The omcS mRNA consisted primarily of a monocistronic transcript, and to a lesser extent, a longer transcript that also contained the downstream gene omcT , which is predicted to encode a second hexaheme outer membrane cytochrome with 62.6% amino acid sequence identity to OmcS. The other abundant c -type cytochrome sheared from the outer surface of G. sulfurreducens , designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetraheme c -type cytochrome. When either omcS or omcE was deleted, G. sulfurreducens could no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. The mutants could reduce Fe(III) in Fe(III) oxide medium only if the Fe(III) chelator, nitrilotriacetic acid, or the electron shuttle, anthraquinone 2,6-disulfonate, was added. Expressing omcS or omcE in trans restored the capacity for Fe(III) oxide reduction. OmcT was not detected among the sheared proteins, and genetic studies indicated that G. sulfurreducens could not reduce Fe(III) oxide when omcT was expressed but OmcS was absent. In contrast, Fe(III) oxide was reduced when omcS was expressed in the absence of OmcT. These results suggest that OmcS and OmcE are involved in electron transfer to Fe(III) oxides in G. sulfurreducens . They also emphasize the importance of evaluating mechanisms for Fe(III) reduction with environmentally relevant Fe(III) oxide, rather than the more commonly utilized Fe(III) citrate, because additional electron transfer components are required for Fe(III) oxide reduction that are not required for Fe(III) citrate reduction.

Published
2005

11. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Tsering Wangchuk, Mayank Kumar, Sharon Stavropoulos, James Cuff, Mostafa Benamara, David DeCaprio, Birhane Hagos, Nathaniel Novod, Tashi Lokyitsang, Nyima Norbu, Jennifer Baldwin, Sabrina M. Stone, Catherine Stone, Geneva Young, Osebhajajeme Egbiremolen, Dawa Thoulutsang, Tanya Mihova, Lisa Kim, Julie Sahalie, Jan Macdonald, Amr Abouelleil, Toby Bloom, Yama Cheshatsang, Carolyne Bardeleben, Qing Yu, Berta Blitshteyn, Tuyen T. Nguyen, Tarjei S. Mikkelsen, Edward Grandbois, Claire M. Wade, John E. Major, Filip Rege, Cindy Nguyen, Andrew Barry, Tracey Honan, Pablo Alvarez, Andy Vo, Manuel Garber, Cristyn Kells, Rachel Mittelman, Lucien Oyono, Norbu Dhargay, Sean M. Sykes, Diallo Ferguson, Tyler Aldredge, Tenchoe Nyima, Todd Sparrow, Daniel S. Hagopian, Christophe Hitte, Andreas Heger, Jane E. Wilkinson, Verneda Ray, Peter Rogov, Ewen F. Kirkness, Jill Falk, Robert Nicol, Christopher Patti, Danielle Perrin, Ted Sharpe, Douglas Smith, Peter Olandt, Matthew Breen, Ali Aslam, Cherylyn Smith, Tara Biagi, Diane Gage, Jean L. Chang, Karen Hughes Miller, Valentine Mlenga, Andrea Horn, Jessie Sloan, Claire M. Healy, Adam Wilson, Ngawang Sherpa, Riza M. Daza, David B. Jaffe, Leonid Boguslavskiy, Jody Camarata, Peter Kisner, William H. Lee, Kunsang Dorjee, M. Husby, Sante Gnerre, Kunsang Gyaltsen, Asha Kamat, Jonathan Butler, Terrance Shea, Alicia Franke, Patrick Cooke, Rayale Rameau, Andrew Zimmer, Gary Gearin, Nabil Hafez, Kerri Topham, Kebede Maru, Chris P. Ponting, Jerome Naylor, Yama Thoulutsang, Keith O'Neill, Jinlei Liu, Manolis Kellis, Claude Bonnet, Claudel Antoine, Passang Dorje, Adal Abebe, Tsamla Tsamla, Michael Kleber, Michael Weiand, Audra Goyette, Rachael Thomas, Lisa Zembek, Atanas Mihalev, Daniel Bessette, Helen Vassiliev, Pasang Bachantsang, Adam Navidi, Kathleen Dooley, Caleb Webber, Pierre Tchuinga, Tashi Bayul, Michael Kamal, Heidi G. Parker, Ben Kanga, Kimberly Dooley, Nadia Calixte, Mostafa Ait-zahra, Niall J. Lennon, Ira Topping, Eric S. Lander, Pieter J. deJong, Nicole R. Allen, Peter An, Boris Boukhgalter, Richard Elong, Thomas E. Landers, Anthony Rachupka, Michael Fitzgerald, Lisa Leuper, William Brockman, Marcia Lara, Susan Faro, Elaine A. Ostrander, Joanne Zainoun, Leigh Anne Hunnicutt, Mark J. Daly, Leanne Hughes, April Cook, Patrick Cahill, Sujaa Raghuraman, Manfred Grabherr, Robert K. Wayne, Adam Brown, Xiaohong Liu, Charles Matthews, Scott Anderson, Margaret Priest, Shailendra Yadav, Evan Mauceli, Kerstin Lindblad-Toh, Patricia Ferreira, Yeshi Lokyitsang, Harindra Arachchi, Alexandre Melnikov, Christina Raymond, James Meldrim, Dmitry Khazanovich, Mieke Citroen, Aaron M. Berlin, Alix Chinh Kieu, John Stalker, Francis Galibert, Noah Duffey, Krista Lance, Louis Meneus, Jennifer Ruth Sadler Hall, Choe Norbu, Pema Tenzing, Richard Marabella, Chee-Wye Chin, Karen Foley, Xiaoping Yang, Nga Nguyen, Tenzin Dawoe, Ryan Hegarty, Julie Rogers, Joseph Graham, Chelsea D. Foley, Leonidas Mulrain, Tsering Wangdi, Karin Decktor, Sarah LeVine, Shuli Yang, Dennis C. Friedrich, Tina Goode, Cecil Rise, Teena Mehta, Laura Ayotte, Michele Clamp, Nicole Stange-Thomann, Annie Lui, Edward J. Kulbokas, Pema Phunkhang, Alan Dupes, Elinor K. Karlsson, Lynne Aftuck, Sahal Osman, Abderrahim Farina, Barry O'Neill, Diana M. Shih, Xiaohui Xie, Lester Dorris, Vijay Venkataraman, Benjamin Jester, Sampath Settipalli, Thu Nguyen, Alville Collymore, Klaus-Peter Koepfli, Senait Tesfaye, Nathan Houde, Susan McDonough, Leo Goodstadt, Glen Munson, Georgia Giannoukos, Jeffrey Chu, Nathan B. Sutter, Sheila A. Fisher, Charlien Jones, Michael C. Zody, Jianying Shi, John P. Pollinger, Mechele Sheehan, Stephen M. J. Searle, Fritz Pierre, Jason Blye, Jean-Pierre Leger, and Stuart DeGray

Subjects
Male, Genomics, Single-nucleotide polymorphism, Biology, Genome, Polymorphism, Single Nucleotide, Synteny, Conserved sequence, Evolution, Molecular, Mice, Dogs, Molecular evolution, Animals, Humans, Dog Diseases, Conserved Sequence, Short Interspersed Nucleotide Elements, Genetics, Whole genome sequencing, Multidisciplinary, Dog leukocyte antigen, Haplotype, Rats, Haplotypes, Mutagenesis, biology.protein, Hybridization, Genetic, Female
Abstract

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Published
2005

12. Factors affecting the development of national quality awards.

Author

Kay C Tan, Mei F Wong, Teena Mehta, and Hsien H Khoo

Subjects
AWARDS, TOTAL quality management, DEVELOPING countries, MANAGEMENT controls, PERFORMANCE standards
Abstract

After the successful launch of the Malcolm Baldrige National Quality Award (MBNQA) and European Quality Award (EQA), the governing authorities of many other countries have begun establishing their own national quality award (NQA) programs. Most NQA models are based on the MBNQA and EQA. Other NQA models choose to be unique. This paper compiles differences in the modeling of 53 NQAs found around the world. From the compilation is derived a set of recommended guidelines for the establishment and further development of NQAs. The guidelines include suggestions for either starting up or enhancing existing NQA programs in both developed and developing countries. [ABSTRACT FROM AUTHOR]

Published
2003
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