Bookmark and Share

Jacques  Ravel
 

Jacques Ravel Ph.D.

Academic Title: Professor
Primary Appointment: Microbiology and Immunology
Additional Title(s): Associate Director for Genomics, Institute for Genome Sciences
jravel@som.umaryland.edu
Location: Bio Park II, 6th Floor, 801 West Baltimore St., Baltimore MD 21201
Phone: (410) 706-5674

Personal History:

Jacques Ravel is a leading microbial genomics scientist at the Institute for Genome Sciences (IGS) and an Associate Professor in Microbiology and Immunology at the University of Maryland School of Medicine in Baltimore, Maryland. His research centers on the Human Microbiome Project, an NIH roadmap to sequence and study the human microbiota and their interrelationship with human health. He is also a noted researcher on microbial forensics.

  • B.Sc., 1990, Biology and Chemistry, University of Nancy I, France
  • M.Sc., 1992, Microbiology, University of Nancy I, France
  • Ph.D., 1994-99, Microbial Ecology, University of Maryland at College Park (Dr. Russell Hill, advisor)
  • Post-doctoral fellow, 1999-2002, The Johns Hopkins University, Chemistry Department (Dr. Craig Townsend)
  • Assistant Investigator, 2002-2007, The Institute for Genomic Research (TIGR), Rockville, MD
  • Associate Professor, 2007-present, Institute for Genome Sciences and University of Maryland School of Medicine

Research Interests:

My research focuses on the application of microbial genomics to three main topics: Exploring the human microbiome: ecology and metagenomics, Microbial genome sequence comparative analyses: the making of a genome with a special emphasis on human microbial pathogens, including Bacillus anthracis, Bacillus cereus, Yersinia pestis, Yersinia pseudotuberculosis, Enteropathogenic Escherichia coli (including E. coli 0157:H7 from contaminated food), Shigella spp., and Salmonella sp.; and Chemical genomics: from genes to structure with a emhphasis on the development of novel bioinformatics tools for the analysis of the secondary metabolic potential of microbes. These are being integrated into 2METDB: a knowledge-based predictive tools for secondary metabolism.

My research activities are funded through grants from NIH, NSF, USDA and DoJ.


Publications:

Ravel J, Gajer P, Abdo Z, Schneider GM, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault KA, Perralta L and Forney LJ. 2010. The vaginal microbiome of reproductive age women. Proceedings of the National Academy of Sciences USA. In press.

Wagner DM, Runberg J., Vogler AJ, Lee J, Driebe E, Price LB, Englethaler DM, Fricke WF, Ravel J, and Keim P. 2010. Emerging and Infectious Diseases. In press.

Brotman RM, Ravel J, Cone RA, and Zenilman RM. 2010. Rapid fluctuation of the vaginal microbiota in asymptomatic women measured by Gram Stain Nugent score analysis. Sexually Transmitted Infections. In press.

Forney LJ, Gajer P, Williams CJ, Schneider GM, McCulle SL, Karlebach S, Brotman RM, Davis CC, Ault KA and Ravel J. 2010. Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. Journal of Clinical Microbiology. 48(5): 1741–1748.

Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE and Ravel J. 2010. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. Journal of Bacteriology. 192(6):1685-1699.

Foster JT, Allan GA, Chan AP, Rabinowicz PD, Ravel J, Jackson PJ, and Keim P. 2010. Single Nucleotide Polymorphisms for Assessing Genetic Diversity in Castor Bean (Ricinus communis). BMC Plant Biology. 10:13.

Price LB, Liu CM, Johnson KE, Aziz M, Lau MA, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ and Gray RH. 2010.The effects of circumcision on the penis microbiome. PLoS ONE. 5(1): e8422.

Myers GS, Mathews SA, Eppinger M, Mitchell C, O'Brien KK, White OR, Benahmed F, Brunham RC, Read TD, Ravel J, Bavoil PM, Timms P. 2009. Evidence that human Chlamydia pneumoniae was zoonotically acquired. Journal of Bacteriology 191(23):7225-7233

Fricke WF, Rasko DA and Ravel J.  2009. The role of genomics in the identification, prediction, and prevention of biological threats. PLoS Biology 7(10):e1000217.

Eppinger M, Guo Z, Sebastian Y, Song Y, Lindler LE, Yang R and Ravel J. 2009. Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. Journal of Bacteriology. 191(24):7628-7629.

Schütte UME, Abdo Z, Foster J, Ravel J, Bunge J, Solheim B and Forney LJ. 2009. Bacterial diversity in a glacier foreland of the High Arctic. Molecular Ecology. Sup 1:54-66

Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, Bowers J, Rattray R, Ravel J, Kingsley C, Keim PS, Lazarus GS, Zenilman JM. 2009. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PLoS ONE 4(7):e6462.

Fricke WF, McDermott PF, Mammel MK, Zhao S, Johnson TJ, Rasko DA, Fedorka-Cray PJ, Pedroso A, Whichard JM, LeClerc JE, White DG, Cebula TQ, and Ravel J. 2009. Antimicrobial Resistance-Conferring Plasmids in Salmonella enterica Serovar Kentucky Isolates from Poultry, Similar to Plasmids from Avian Pathogenic Escherichia coli Strains. Applied and Environmental Microbiology 75(18):5963-71. Epub 2009 July 31.

Fricke WF, Welch TJ, McDermott PF, Mammel MK, LeClerc JE, White DG, Cebula TA, Ravel J. 2009. Comparative genomics of the IncA/C multidrug resistance plasmid family. Journal of Bacteriology 191(15):4750-7. Epub 2009 May 29.

Bachmann BO, Ravel J. 2009. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in Enzymology 458:181-217.

Simonson TS, Okinaka RT, Wang B, Easterday WR, Huynh L, U'Ren JM, Dukerich M, Zanecki SR, Kenefic LJ, Beaudry J, Schupp JM, Pearson T, Wagner DM, Hoffmaster A, Ravel J and Keim P. 2009. Bacillus anthracis in China and its relationship to worldwide lineages. BMC Microbiology. 9:71.

Kenefic LJ, Pearson T, Okinaka RT, Schupp JM, Wagner DM, Ravel J, Hoffmaster AR, Trim CP, Chung W-K, Beaudry JA, Foster JT, Mead JI, Keim P. 2009. Pre-columbian origins for north american anthrax. PLoS ONE. 4(3): e4813.

Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA. 2009 The complete genome sequence of Bacillus anthracis Ames "Ancestor". Journal of Bacteriology. 191(1):445-6.

Fricke WF, Wright MS, Lindell AH, Harkins DA, Baker-Austin C, Ravel J* and R Stepanauskas. 2008. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate E. coli SMS-3-5. Journal of Bacteriology. 190(20):6779-94. (*senior and corresponding author)

Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sperandio V, Ravel J. 2008. The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology. 190(20):6881-93.

Brotmann, R.M. and J. Ravel. 2008. Ready or not: the molecular diagnosis of bacterial vaginosis. Clinical Infectious Diseases. 47(1):44-6.

Donia MS, Ravel J, Schmidt EW. A global assembly line for cyanobactins. 2008. Nature Chemical Biology. 4(6):341-3. Epub 2008 Apr 20.

S.E. Schutzer, L.R.K. Schlater, C.M. Ronning, D. DeShazer, B.J. Luft, J.J. Dunn, J. Ravel, C.M. Fraser-Liggett, and W.C. Nierman. 2008. Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from select agent lists. PLoS ONE. 2008; 3(4): e2058.

K.E. Wommack, J. Bahsvar and J. Ravel. 2008. Metagenomics: Read size matters. Applied and Environmental Microbiology. 74(5):1453-1463.

M. Eppinger, MJ Rosovitz, W.F. Fricke, D.A. Rask, G. Korkorina, C. Fayolle, L.E. Lindler, E. Carniel, J. Ravel. 2007. Genome Sequence of Y. pseudotuberculosis IP31758, the causative agent of Far East Scarlet Like Fever (FESLF): Linking Genomic Plasticity to Pathogenicity. 2007. PLoS Genetics. 3(8): e142.

T.J. Welch, W.F. Fricke, M.-L. Rosso, D.A. Rasko, M.K. Mammel, M. Eppinger, MJ Rosovitz, D.G. White, P.F. McDermott, D. Wagner, L. Rahalison, J.E. LeClerc, J.M. Hinshaw, L.E. Lindler, T.A. Cebula, E. Carniel and J. Ravel. 2007. Multiple antimicrobial resistance in Plague: an emerging risk. PLoS ONE. 2(3): e309.

Rasko DA, Rosovitz MJ, Okstad OA, Fouts DE, Jiang L, Cer RZ, Kolsto AB, Gill SR, Ravel J. 2007. Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus group plasmids including B. anthracis pXO1. Journal of Bacteriology 189:52-64.

R. Auerbach, A. Tuanyok, W. Probert, L. Kenefic, A. Vogler, D. Bruce, C. Munk, T. Brettin, M. Eppinger, J. Ravel, D. Wagner and P.l Keim. 2007. Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. PLoS ONE. 2(8): e770.

K. Lee, D.N. Barker, J. Ravel, R. Auerbach, D. Wagner, P. Keim and J.G. Leid. 2007. Phenotypic and functional characterization of Bacillus anthracis biofilms. Microbiology. 153(6):1693-701.

M.N. Van Ert, W.R. Easterday, L.Y. Huynh, M.E. Hugh-Jones, J. Ravel, S.R. Zanecki, T. Pearson, T.S. Simonson, J.M. U'ren, S.M. Kachur, R.R. Leadem, S.D. Rhoton, G. Zinser, J. Farlow, P.R. Coker, K.L. Smith, B. Wang, L.J. Kenefic, C.M. Fraser, D.M. Wagner, and P. Keim. 2007. Global Genetic Population Structure of Bacillus anthracis. PLoS ONE. 2(5):e461.

Van Ert MN, Easterday WR, Simonson TS, U'ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB, Beaudry J, Welty-Bernard A, Read T, Fraser CM, Ravel J, Keim P. 2007. Strain-specific single nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology. 45(1):47-53.

Donia M., Hathaway B.J., Sudek S., Haygood M.G., Rosovitz M.J., Ravel J., and Schmidt E.W. 2006. Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nature Chemical Biology. 2(12):729-35.

Paulsen I.T., Press C., Ravel J., Kobayashi D.Y., Myers G.S.A., Mavrodi D.V., DeBoy R.T., Seshadri R., Ren Q., Madupu R., Dodson R.J., Durkin A.S., Brinkac L.M., Daugherty S.C., Sullivan S.A., Rosovitz M.J., Gwinn M.L., Zhou L., Nelson W.C., Weidman J., Watkins K., Tran K., Khouri H., Pierson E.A., Pierson L.S. III, Thomashow L.S., and Loper J.E. 2006. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5: insights into the biological control of plant disease. Nature Biotechnology. 23:873-878.

Schmidt E.W., Nelson J.T., Rasko D,A., Sudek S., Eisen, J.A., Haygood, M.G. and Ravel J. 2005. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proceedings of the National Academy of Sciences USA. 102(20):7315-7320.

Rasko D.A., Myers G.S., Ravel J. 2005. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics. 6(1):2.

Ravel J. and C.M. Fraser. 2005. Genomics at the genus scale. Trends in Microbiology. 13(3)94-96.

T. Pearson, J. Busch, J. Ravel, T.D. Read, S. Rhoton, J. U'ren, T. Simonson, S. Kachur, R. Leadem, M. Cardon, M. Van Ert, L. Huynh, C.M. Fraser and P. Keim. 2004. Phylogenetic discovery bias in Bacillus anthracis using single nucleotide polymorphisms from whole genome sequencing. Proceedings of the National Academy of Sciences USA. 101(37):13536-13541.

Hoffmaster, A.R., J. Ravel, D.A. Rasko, G.D. Chapman, M. Chute C.K. Marston, B.K. De, C.T. Sachhi, C. Fitzgerald, L.W. Mayer, M.C.J. Maiden, F.G. Priest, M. Barker, Lingxia Jiang, R.Z. Cer, J. Rilstone, S.N. Peterson, R.S. Weyant, R. Galloway, T.D. Read, T. Popovic and C.M. Fraser. 2004. Discovery of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax: public health challenges in the age of bioterrorism. Proceedings of the National Academy of Sciences USA. 101(22):8449:8454.