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Jacques Ravel, PhD

Academic Title:

Professor

Primary Appointment:

Microbiology and Immunology

Administrative Title:

Associate Director, Institute For Genome Sciences

Additional Title:

Associate Director for Genomics, Institute for Genome Sciences

Location:

Health Sciences Facility III, 670 West Baltimore St, Baltimore 21201

Phone (Primary):

(410) 706-5674

Education and Training

  • 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, 2007-2012, Dept. Microbiology and Immunology, University of Maryland School of Medicine
  • Professor, 2012-present, Dept. Microbiology and Immunology, University of Maryland School of Medicine
  • Associate Director for Genomics, 2010-present, Institute for Genome Sciences, University of Maryland School of Medicine

Biosketch

Dr. Ravel is the Associate Director for Genomics at the Institute for Genome Sciences (IGS) (www.igs.som.umaryland.edu) and a Professor of Microbiology and Immunology at the University of Maryland School of Medicine in Baltimore, Maryland. He received his Ph.D. degree from the University of Maryland College Park in Environmental Molecular Microbiology and Ecology and performed his postdoctoral training at the Johns Hopkins University in the Department of Chemistry working on microbial natural product chemistry.

Before accepting his current position in 2007, Dr. Ravel was an Assistant Investigator at the Institute for Genomic Research (TIGR) in Rockville, MD, the institute where the first microbial genome was sequenced in 1995. He was elected to the American Academy of Microbiology in 2012 and in 2015, he was awarded the Blaise Pascal International Research Chair (www.chaires-blaise-pascal.ens.fr). Dr. Ravel is the Editor in Chief of the journal Microbiome (www.microbiomejournal.com) and an Associated Editor for the journal mBio.

Highlighted Publications

Bradford LL, Ravel J. 2016. The vaginal mycobiome: a poorly understood contributor to women's health and diseases. Virulence. 2016 Sep 22:0.

Robinson CK, Brotman RM, Ravel J. Intricacies of assessing the human microbiome in epidemiologic studies. Annals of Epidemiology. 2016 26(5):311-21.

Ravel J, Brotman RM. 2016. Translating the vaginal microbiome: gaps and challenges. Genome Medicine. 8:35.

Smith SB, Ravel J. 2016. The vaginal microbiota, host defense and reproductive physiology. Journal of Physiology. DOI: 10.1113/JP271694.

Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: a proposal. Microbiome 3:31.

Nunn KL, Wang Y-Y, Harit D, Humphrys MS, Ma B, Cone R, Ravel J, Lai SK. 2015 Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota. mBio. 6(5):e01084-15

Additional Publication Citations

A complete list of Dr. Ravel's 177 publications can be found here:

https://www.ncbi.nlm.nih.gov/sites/myncbi/1fSS3RRbN7lQ1/bibliography/40012322/public/?sort=date&direction=descending

Neuendorf E., Gajer P, Bowlin AK, Marques PX, Ma B, Yang H, Fu L, Humphrys MS, Forney LJ, Myers GSA, Bavoil PM, Rank RG, Ravel J. 2015. Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota. Pathogens and Disease.

Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Bieda J, Chaemsaithong P, Miranda J, Chaiworapongsa T, and Ravel J. 2014.The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term. Microbiome, 2:18.

Fadrosh D, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. 2014. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome. 2(1):6.

Romero R, Hassan S, Gajer P, Tarca A, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J, Chaiworapongsa T and Ravel J. 2014. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome. 2(1):4.

Ravel J, Brotman RM, Gajer P, Ma B, Nandy M, Fadrosh DW, Sakamoto J, Koenig SSK, Fu L, Zhou Z, Hickey RJ, Schwebke JR
and Forney LJ. 2013. Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome 1:29.

Hoffmann DE, Fraser CM, Palumbo FB, Ravel J, Rothenberg K, Rowthorn V, SchwartzJ. 2013. Probiotics: Finding the right regulatory balance. Science. 342(6156):314-315.

Hoffmann DE, Fortenberry JD, Ravel J. 2013. Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics. 41(2):454–469.

Bradford LL, Ravel J, Bruno V. 2013. Understanding vulvovaginal Candidiasis through a community genomics approach. Current Fungal Infection Reports. 7(2):126-131

Ravel J, Gajer P, Fu L, MauckCK, Koenig SSK, Sakamoto J, Motsinger-Reif AA, Doncel GF, Zeichner SL. 2012. Twice-Daily Applications of HIV Microbicides Alter the Vaginal Microbiota. mBio 3(6):e00370-12

Methé B, Nelson K, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF et al., Ravel J, et al., White O (HMP Consortium). 2012. A framework for human microbiome research. Nature. 486:215-221.

Huttenhower C, Gevers D, Knight R, Abubuker S, Badger JH, Chinwalla AT, et al., Ravel J., et al. White O (HMP Consortium). 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486:207-214.

Brotman RM, Bradford LL, Conrad M, Gajer P, Ault KA, Peralta L, Forney LJ, Carlton JM, Abdo Z,and Ravel J. 2012. Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Sexually Transmitted Diseases. 39(10):807-812.

Gajer P, Brotman RM, Bai G, Sakamoto J, Shutte UME, Zhong X, Koenig SSK, Fu L, Ma Z, Zhou X, Abdo Z, Forney LJ and Ravel J. 2012. The temporal dynamics of the vaginal microbiota. Science Translational Medicine. 4, 132ra52.

Ma B, Forney LJ and Ravel J. 2012. The vaginal microbiota: Rethinking health and diseases. Annual Review of Microbiology. 66:371–89.

Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ. 2012. Understanding vaginal microbiome complexity from an ecological perspective. Translational Research. 160(4):267-82.

Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SSK, Sakamoto J, Boothe D, Gicquelais R, Kryszak D, Puppa E, Catassi C, Ravel J, Fasano A. 2012. Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS ONE. 7(3):e33387.

Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J. 2012. Origin and variation of tunicate secondary metabolites. Journal of Natural Products. 75:294-304.

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N Gordon, JI and Knight, R. 2011. Moving pictures of the human microbiome. Genome Biology, 12(5):R50.

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. 108 Suppl 1:4680-7.

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. 86: 297-302.

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 anthracisAmes 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.

Research Interests

Dr. Ravel's research program (www.ravel-lab.org) focuses on applying modern genomics technologies and ecological principles to characterize the role and dynamics of the microbial communities inhabiting the human body in health and disease and better define the interactions between the host, the microbes and the environment that drive these ecological systems. Specifically, he is interested in deciphering the role of the vaginal microbiome in women's health using clinical genomics and systems biology approaches, in order to develop improved strategy to manage gynecological and obstetrics conditions.

He is the co-Director of the NIH funded Collaborative Research Center on Sexually Transmitted Diseases entitled "Ecopathogenomics of Sexually Transmitted Diseases (EPSTI – epsti.org)" which aims at applying systems biology approaches to examine the triangular relationship between human genetic variation, sexually transmitted infections and co-infections caused by Chlamydia trachomatis and Neisseria gonorrhoeae, and the function of the vaginal microbiome. In addition, he is principal investigator or co-investigator on several NIH grants that aim at understanding the interactions between the vaginal microbiome, the environment and the host in the context of preterm initiation of labor.

Grants and Contracts

R01 NR015495-01 Ravel)
05/13/2016 – 02/28/2021
Elucidating causes of vaginal symptoms using a multi-omics approach

R01 NR014784-03 (Ravel/Elovitz)
09/28/2013 – 06/30/2018
Revealing the role of the cervico-vaginal microbiome in spontaneous preterm birth

R01 NR014826-03 Ravel/Regan)
09/28/2013 - 06/30/2018
The Influence of modifiable factor on the vaginal microbiota and preterm birth

U19 AI084044-07 (Ravel/Bavoil)
09/01/2014 – 08/31/2019
Ecopathogenomics of sexually transmitted infections (EPSTI)

R01 AI116799-01 (Brotman/Ravel)
05/01/2015 – 04/30/2020
Longitudinal Study of the Vaginal Microbiome Prior to Incident STI

R21 AI119633A (Hoffmann)
07/01/2015 - 6/30/2017
Microbiota Transplantation: Recommendations for a Regulatory Framework

R01 AI119012 (Brotman)
02/05/2016 – 01/31/2021
Lubricant Use and the Vaginal Microbiome