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Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. The COMBREX project: design, methodology, and initial results. PLoS Biol 2013; 11:e1001638. [PMID: 24013487 PMCID: PMC3754883 DOI: 10.1371/journal.pbio.1001638] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Brian P. Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail: (BPA); (SK)
| | - Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Peter Brown
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Han-Pil Choi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Lina L. Faller
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Jyotsna Guleria
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Niels Klitgord
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Ami Levy-Moonshine
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Almaz Maksad
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Mark McGettrick
- Diatom Software LLC, Holliston, Massachusetts, United States of America
| | - Lais Osmani
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Revonda Pokrzywa
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - John Rachlin
- Diatom Software LLC, Holliston, Massachusetts, United States of America
| | - Rajeswari Swaminathan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Benjamin Allen
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Genevieve Housman
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Caitlin Monahan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Krista Rochussen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Kevin Tao
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Ashok S. Bhagwat
- Department of Chemistry, Wayne State University, Detroit, Michigan, United States of America
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Donald Ferguson
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Alexey Fomenkov
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
| | - Richard D. Morgan
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Andrei L. Osterman
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Dmitry A. Rodionov
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Irina A. Rodionova
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Kenneth E. Rudd
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida, United States of America
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - James Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shuang-yong Xu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alex Bateman
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Robert M. Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo, Toledo, Ohio, United States of America
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Woo-Suk Chang
- Department of Biology, University of Texas-Arlington, Arlington, Texas, United States of America
| | - Manuel Ferrer
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Michael Y. Galperin
- National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Julien Gobeill
- Department of Library and Information Sciences, University of Applied Sciences Western Switzerland, Geneva, Switzerland
- Bibliomics and Text Mining Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Daniel Haft
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - John Hunt
- Biological Sciences, Columbia University, New York, New York, United States of America
| | - Peter Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, California, United States of America
| | - William Klimke
- National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dana Macelis
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ramana Madupu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Maria J. Martin
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Jeffrey H. Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Claire O'Donovan
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Patrick Ruch
- Department of Library and Information Sciences, University of Applied Sciences Western Switzerland, Geneva, Switzerland
- Bibliomics and Text Mining Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Aaron Setterdahl
- Department of Chemistry, Indiana University Southeast, New Albany, Indiana, United States of America
| | - Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - John Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Alexander Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Dmitri Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Germán Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, Structural, and Genetic Studies, Columbia University, New York, New York, United States of America
| | - Jie Hu
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - David Horn
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Kimmen Sjölander
- Berkeley Phylogenomics Group, University of California, Berkeley, California, United States of America
| | - Steven L. Salzberg
- Departments of Medicine and Biostatistics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dennis Vitkup
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Stanley Letovsky
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Charles DeLisi
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Richard J. Roberts
- New England Biolabs, Ipswich, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Martin Steffen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- * E-mail: (BPA); (SK)
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Lebreton F, van Schaik W, Manson McGuire A, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJL, Earl AM, Gilmore MS. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. mBio 2013; 4:e00534-13. [PMID: 23963180 PMCID: PMC3747589 DOI: 10.1128/mbio.00534-13] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/23/2013] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Enterococcus faecium, natively a gut commensal organism, emerged as a leading cause of multidrug-resistant hospital-acquired infection in the 1980s. As the living record of its adaptation to changes in habitat, we sequenced the genomes of 51 strains, isolated from various ecological environments, to understand how E. faecium emerged as a leading hospital pathogen. Because of the scale and diversity of the sampled strains, we were able to resolve the lineage responsible for epidemic, multidrug-resistant human infection from other strains and to measure the evolutionary distances between groups. We found that the epidemic hospital-adapted lineage is rapidly evolving and emerged approximately 75 years ago, concomitant with the introduction of antibiotics, from a population that included the majority of animal strains, and not from human commensal lines. We further found that the lineage that included most strains of animal origin diverged from the main human commensal line approximately 3,000 years ago, a time that corresponds to increasing urbanization of humans, development of hygienic practices, and domestication of animals, which we speculate contributed to their ecological separation. Each bifurcation was accompanied by the acquisition of new metabolic capabilities and colonization traits on mobile elements and the loss of function and genome remodeling associated with mobile element insertion and movement. As a result, diversity within the species, in terms of sequence divergence as well as gene content, spans a range usually associated with speciation. IMPORTANCE Enterococci, in particular vancomycin-resistant Enterococcus faecium, recently emerged as a leading cause of hospital-acquired infection worldwide. In this study, we examined genome sequence data to understand the bacterial adaptations that accompanied this transformation from microbes that existed for eons as members of host microbiota. We observed changes in the genomes that paralleled changes in human behavior. An initial bifurcation within the species appears to have occurred at a time that corresponds to the urbanization of humans and domestication of animals, and a more recent bifurcation parallels the introduction of antibiotics in medicine and agriculture. In response to the opportunity to fill niches associated with changes in human activity, a rapidly evolving lineage emerged, a lineage responsible for the vast majority of multidrug-resistant E. faecium infections.
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Affiliation(s)
| | | | | | - Paul Godfrey
- The Broad Institute, Cambridge, Massachusetts, USA
| | | | | | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Lu Cheng
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Sakina Saif
- The Broad Institute, Cambridge, Massachusetts, USA
| | - Sarah Young
- The Broad Institute, Cambridge, Massachusetts, USA
| | | | | | - Bruce Birren
- The Broad Institute, Cambridge, Massachusetts, USA
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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7
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Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PLoS One 2013; 8:e66605. [PMID: 23825549 PMCID: PMC3688963 DOI: 10.1371/journal.pone.0066605] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/08/2013] [Indexed: 12/16/2022] Open
Abstract
The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate using derivatized nano-particles, and subsequent identification by mass spectrometry. Candidate genes encoding these proteins were cloned and expressed in Escherichia coli, and the recombinant proteins were purified and characterized biochemically and their biochemical parameters compared with the native ones. These proteins include a guanosine triphosphate (GTP) cyclohydrolase (HP0959), an ATPase (HP1079), an adenosine deaminase (HP0267), a phosphodiesterase (HP1042), an aminopeptidase (HP1037), and new substrates were characterized for a peptidoglycan deacetylase (HP0310). Generally, characterized enzymes were active at acidic to neutral pH (4.0–7.5) with temperature optima ranging from 35 to 55°C, although some exhibited outstanding characteristics.
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Affiliation(s)
- Han-Pil Choi
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Silvia Juarez
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Sergio Ciordia
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Marisol Fernandez
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Rafael Bargiela
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
| | - Juan P. Albar
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Brian P. Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Simon Kasif
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Manuel Ferrer
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
- * E-mail: (MS); (MF)
| | - Martin Steffen
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Dept of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail: (MS); (MF)
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8
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Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 2012; 7:e37919. [PMID: 22675498 PMCID: PMC3366996 DOI: 10.1371/journal.pone.0037919] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/30/2012] [Indexed: 11/18/2022] Open
Abstract
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
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Affiliation(s)
- Bo Liu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
| | - Lina L. Faller
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Niels Klitgord
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Mohammad Ghodsi
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
| | - Daniel D. Sommer
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Theodore R. Gibbons
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, United States of America
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- The McKusick-Nathans Institute for Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Shan Li
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - O. Colin Stine
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hatice Hasturk
- The Forysth Institute, Department of Periodontology, Cambridge, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Children’s Informatics Program, Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, United States of America
| | - Salomon Amar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Center for Anti-Inflammatory Therapeutics; Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
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