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801 West Baltimore Street
Baltimore, MD 21201

The Laboratory of Dr. Jacques Ravel at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. Dr. Ravel research is on the role of the vaginal microbiome in women's health. 




  • Breshears LM, Edwards VL, Ravel J, Peterson ML. 2015. Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model. BMC Microbiology 15(1):276.
  • 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.
  • Nelson TM, Borgogna J-LC, Brotman RM, Ravel J, Walk ST, Yeoman CJ. 2015. Vaginal biogenic amines: biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis? Frontiers in Physiology  6:253.
  • Yu G, Fadrosh D, Goedert JJ, Ravel J, Goldstein AM. 2015. Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets. PLoS ONE, 10:e0132253.
  • Flores R, Shi J, Yu G, Ma B, Ravel J, Goedert JJ, Sinha R. 2015. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome 3:33.
  • Goedert JJ, Gong Y, Hua X, Zhon H, He Y, Peng P, Yu G, Wang W, Ravel J, Shi J, Zheng Y. 2015. Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening. 2015. A Population-based Study. EBioMedicine. 2(6):597–603.
  • Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015 3:31. doi: 10.1186/s40168-015-0094-5. eCollection 2015. PubMed PMID: 26229597; PubMed Central PMCID: PMC4520061.
  • Robinson CK, Wierzchos J, Black C, Crits-Christoph A, Ma B, Ravel J, Ascaso C, Artieda O, Valea S, Roldan M et al: Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert. Environmental Microbiology 2015, 17(2):299-315.
  • Neuendorf E, Gajer P, Bowlin AK, Marques PX, Ma B, Yang H, Fu L, Humphrys MS, Forney LJ, Myers GS et al: Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota. Pathogens and Disease 2015, 73(4).
  • Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N: Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 2015.
  • Mojica SA, Hovis KM, Frieman MB, Tran B, Hsia RC, Ravel J, Jenkins-Houk C, Wilson KL, Bavoil PM: SINC, a type III secreted protein of Chlamydia psittaci, targets the inner nuclear membrane of infected cells and uninfected neighbors. Molecular biology of the cell 2015, 26(10):1918-1934.
  • Mendes-Soares H, Krishnan V, Settles ML, Ravel J, Brown CJ, Forney LJ: Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. Pathogens and disease 2015, 73(4).
  • Mehta SD, Donovan B, Weber KM, Cohen M, Ravel J, Gajer P, Gilbert D, Burgad D, Spear GT: The vaginal microbiota over an 8- to 10-year period in a cohort of HIV-infected and HIV-uninfected women. PloS one 2015, 10(2):e0116894.
  • Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J et al: New signaling pathways govern the host response to C. albicans infection in various niches. Genome research 2015, 25(5):679-689.
  • Liu CM, Hungate BA, Tobian AA, Ravel J, Prodger JL, Serwadda D, Kigozi G, Galiwango RM, Nalugoda F, Keim P et al: Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda. mBio 2015, 6(3).
  • Goedert JJ, Jones G, Hua X, Xu X, Yu G, Flores R, Falk RT, Gail MH, Shi J, Ravel J et al: Investigation of the association between the fecal microbiota and breast cancer in postmenopausal women: a population-based case-control pilot study. Journal of the National Cancer Institute 2015, 107(8).
  • Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, Mahurkar A, Ravel J, Haverkamp M, Fiorino AM, Botelho C et al: Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 2015, 6(2).
  • Dareng EO, Ma B, Famooto AO, Akarolo-Anthony SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H et al: Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women. Epidemiology and infection 2015:1-15.


  • Yu G, Fadrosh D, Ma B, Ravel J, Goedert JJ: Anal microbiota profiles in HIV-positive and HIV-negative MSM. AIDS (London, England) 2014, 28(5):753-760.
  • Yeruva L, Myers GS, Spencer N, Creasy HH, Adams NE, Maurelli AT, McChesney GR, Cleves MA, Ravel J, Bowlin A et al: Early microRNA expression profile as a prognostic biomarker for the development of pelvic inflammatory disease in a mouse model of chlamydial genital infection. mBio 2014, 5(3):e01241-01214.
  • Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L et al: An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. AIDS research and human retroviruses 2014, 30(11):1046-1054.
  • Sanjar F, Hazen TH, Shah SM, Koenig SS, Agrawal S, Daugherty S, Sadzewicz L, Tallon LJ, Mammel MK, Feng P et al: Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States. Genome announcements 2014, 2(1).
  • Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J et al: The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2014, 2(1):4.
  • Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J et al: Correction: The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2014, 2(1):10.
  • Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Bieda J, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J: The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term. Microbiome 2014, 2:18.
  • Ravel J, Wommack KE: Thank you to Microbiome's peer reviewers in 2013. Microbiome 2014, 2(1):2.
  • Ravel J, Wommack KE: All hail reproducibility in microbiome research. Microbiome 2014, 2(1):8.
  • Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT: Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PloS one 2014, 9(3):e90517.
  • Mirmonsef P, Hotton AL, Gilbert D, Burgad D, Landay A, Weber KM, Cohen M, Ravel J, Spear GT: Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH. PloS one 2014, 9(7):e102467.
  • Marsan D, Wommack KE, Ravel J, Chen F: Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary. Genome announcements 2014, 2(1).
  • Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G et al: Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PloS one 2014, 9(7):e102651.
  • Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE et al: Advancing the microbiome research community. Cell 2014, 159(2):227-230.
  • Hoffmann DE, Fraser CM, Palumbo F, Ravel J, Rowthorn V, Schwartz J: Probiotics: achieving a better regulatory fit. Food and drug law journal 2014, 69(2):237-272, ii.
  • Fuhrman BJ, Feigelson HS, Flores R, Gail MH, Xu X, Ravel J, Goedert JJ: Associations of the fecal microbiome with urinary estrogens and estrogen metabolites in postmenopausal women. The Journal of clinical endocrinology and metabolism 2014, 99(12):4632-4640.
  • Feigelson HS, Bischoff K, Ardini MA, Ravel J, Gail MH, Flores R, Goedert JJ: Feasibility of self-collection of fecal specimens by randomly sampled women for health-related studies of the gut microbiome. BMC research notes 2014, 7:204.
  • Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J: An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2014, 2(1):6.
  • Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J et al: Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio 2014, 5(6):e01721.
  • Broutet N, Fruth U, Deal C, Gottlieb SL, Rees H: Vaccines against sexually transmitted infections: the way forward. Vaccine 2014, 32(14):1630-1637.
  • Brotman RM, Shardell MD, Gajer P, Tracy JK, Zenilman JM, Ravel J, Gravitt PE: Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. The Journal of infectious diseases 2014, 210(11):1723-1733.
  • Brotman RM, Shardell MD, Gajer P, Fadrosh D, Chang K, Silver MI, Viscidi RP, Burke AE, Ravel J, Gravitt PE: Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. Menopause (New York, NY) 2014, 21(5):450-458.
  • Brotman RM, Ravel J, Bavoil PM, Gravitt PE, Ghanem KG: Microbiome, sex hormones, and immune responses in the reproductive tract: challenges for vaccine development against sexually transmitted infections. Vaccine 2014, 32(14):1543-1552.
  • Brotman RM, He X, Gajer P, Fadrosh D, Sharma E, Mongodin EF, Ravel J, Glover ED, Rath JM: Association between cigarette smoking and the vaginal microbiota: a pilot study. BMC infectious diseases 2014, 14:471.


  • Wommack KE, Ravel J: Microbiome, demystifying the role of microbial communities in the biosphere. Microbiome 2013, 1(1):1.
  • Ravel J, Brotman RM, Gajer P, Ma B, Nandy M, Fadrosh DW, Sakamoto J, Koenig SS, Fu L, Zhou X et al: Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome 2013, 1(1):29.
  • Planet PJ, Rampersaud R, Hymes SR, Whittier S, Della-Latta PA, Narechania A, Daugherty SC, Santana-Cruz I, Desalle R, Ravel J et al: Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1. Genome announcements 2013, 1(1).
  • Liu CM, Hungate BA, Tobian AA, Serwadda D, Ravel J, Lester R, Kigozi G, Aziz M, Galiwango RM, Nalugoda F et al: Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria. mBio 2013, 4(2):e00076.
  • Hovis KM, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank RG, Myers GS, Ravel J, Hsia RC, Bavoil PM: Genus-optimized strategy for the identification of chlamydial type III secretion substrates. Pathogens and disease 2013, 69(3):213-222.
  • Hoffmann DE, Fraser CM, Palumbo FB, Ravel J, Rothenberg K, Rowthorn V, Schwartz J: Science and regulation. Probiotics: finding the right regulatory balance. Science (New York, NY) 2013, 342(6156):314-315.
  • Hoffmann DE, Fortenberry JD, Ravel J: 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 2013, 41(2):454-469.
  • Eppinger M, Daugherty S, Agrawal S, Galens K, Sengamalay N, Sadzewicz L, Tallon L, Cebula TA, Mammel MK, Feng P et al: Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome announcements 2013, 1(2):e0013412.


  • Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ: Evaluation of methods for the extraction and purification of DNA from the human microbiome. PloS one 2012, 7(3):e33865.
  • Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SS, Sakamoto J, Boothe D et al: Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PloS one 2012, 7(3):e33387.
  • Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J: Origin and variation of tunicate secondary metabolites. Journal of natural products 2012, 75(2):295-304.
  • Ravel J, Gajer P, Fu L, Mauck CK, Koenig SS, Sakamoto J, Motsinger-Reif AA, Doncel GF, Zeichner SL: Twice-daily application of HIV microbicides alter the vaginal microbiota. mBio 2012, 3(6).
  • Macklaim JM, Cohen CR, Donders G, Gloor GB, Hill JE, Parham GP, Ravel J, Spear G, van de Wijgert J, Reid G: Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease. Reproductive sciences (Thousand Oaks, Calif) 2012, 19(11):1154-1162.
  • Ma B, Forney LJ, Ravel J: Vaginal microbiome: rethinking health and disease. Annual review of microbiology 2012, 66:371-389.
  • Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ: Understanding vaginal microbiome complexity from an ecological perspective. Translational research : the journal of laboratory and clinical medicine 2012, 160(4):267-282.
  • Hasan NA, Choi SY, Eppinger M, Clark PW, Chen A, Alam M, Haley BJ, Taviani E, Hine E, Su Q et al: Genomic diversity of 2010 Haitian cholera outbreak strains. Proceedings of the National Academy of Sciences of the United States of America 2012, 109(29):E2010-2017.
  • Gajer P, Brotman RM, Bai G, Sakamoto J, Schutte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X et al: Temporal dynamics of the human vaginal microbiota. Science translational medicine 2012, 4(132):132ra152.
  • Flores R, Shi J, Gail MH, Ravel J, Goedert JJ: Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities. European journal of clinical investigation 2012, 42(8):848-854.
  • Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ: Association of fecal microbial diversity and taxonomy with selected enzymatic functions. PloS one 2012, 7(6):e39745.
  • Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ: Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. European journal of clinical investigation 2012, 42(8):855-863.
  • Flores R, Shi J, Fuhrman B, Xu X, Veenstra TD, Gail MH, Gajer P, Ravel J, Goedert JJ: Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study. Journal of translational medicine 2012, 10:253.
  • Eppinger M, Radnedge L, Andersen G, Vietri N, Severson G, Mou S, Ravel J, Worsham PL: Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance. PloS one 2012, 7(3):e32911.
  • Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J: Whole-genome sequences of Bacillus subtilis and close relatives. Journal of bacteriology 2012, 194(9):2378-2379.
  • Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J: Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Sexually transmitted diseases 2012, 39(10):807-812.
  • Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM: Comparison of storage conditions for human vaginal microbiome studies. PloS one 2012, 7(5):e36934.
  • Structure, function and diversity of the healthy human microbiome. Nature 2012, 486(7402):207-214.
  • A framework for human microbiome research. Nature 2012, 486(7402):215-221.


  • Zan J, Fricke WF, Fuqua C, Ravel J, Hill RT: Genome sequence of Ruegeria sp. strain KLH11, an N-acylhomoserine lactone-producing bacterium isolated from the marine sponge Mycale laxissima. Journal of bacteriology 2011, 193(18):5011-5012.
  • Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G et al: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature biotechnology 2011, 29(5):415-420.
  • Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW et al: Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS neglected tropical diseases 2011, 5(9):e1319.
  • Rivarola M, Foster JT, Chan AP, Williams AL, Rice DW, Liu X, Melake-Berhan A, Huot Creasy H, Puiu D, Rosovitz MJ et al: Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PloS one 2011, 6(7):e21743.
  • Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO et al: Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences of the United States of America 2011, 108 Suppl 1:4680-4687.
  • Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD et al: Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(12):5027-5032.
  • Price LB, Liu CM, Frankel YM, Melendez JH, Aziz M, Buchhagen J, Contente-Cuomo T, Engelthaler DM, Keim PS, Ravel J et al: Macroscale spatial variation in chronic wound microbiota: a cross-sectional study. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society 2011, 19(1):80-88.
  • Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE: Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied and environmental microbiology 2011, 77(22):8071-8079.
  • Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, Leclerc JE, Ravel J, Cebula TA: Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. Journal of bacteriology 2011, 193(14):3556-3568.
  • Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA: Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir. Applied and environmental microbiology 2011, 77(9):2916-2925.
  • Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA: Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(50):20142-20147.
  • Eppinger M, Bunk B, Johns MA, Edirisinghe JN, Kutumbaka KK, Koenig SS, Creasy HH, Rosovitz MJ, Riley DR, Daugherty S et al: Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. Journal of bacteriology 2011, 193(16):4199-4213.
  • Dumas MD, Polson SW, Ritter D, Ravel J, Gelb J, Jr., Morgan R, Wommack KE: Impacts of poultry house environment on poultry litter bacterial community composition. PloS one 2011, 6(9):e24785.
  • Du Y, Derewacz DK, Deguire SM, Teske J, Ravel J, Sulikowski GA, Bachmann BO: Biosynthesis of the Apoptolidins in Nocardiopsis sp. FU 40. Tetrahedron 2011, 67(35):6568-6575.
  • Donia MS, Fricke WF, Ravel J, Schmidt EW: Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PloS one 2011, 6(3):e17897.
  • Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG et al: Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(51):E1423-1432.
  • Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N et al: Moving pictures of the human microbiome. Genome biology 2011, 12(5):R50.


  • Zhou X, Brotman RM, Gajer P, Abdo Z, Schuette U, Ma S, Ravel J, Forney LJ: Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Infectious diseases in obstetrics and gynecology 2010, 2010:737425.
  • Wagner DM, Runberg J, Vogler AJ, Lee J, Driebe E, Price LB, Engelthaler DM, Fricke WF, Ravel J, Keim P: No resistance plasmid in Yersinia pestis, North America. Emerging infectious diseases 2010, 16(5):885-887.
  • Schutte UM, Abdo Z, Foster J, Ravel J, Bunge J, Solheim B, Forney LJ: Bacterial diversity in a glacier foreland of the high Arctic. Molecular ecology 2010, 19 Suppl 1:54-66.
  • Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J: Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and environmental microbiology 2010, 76(16):5636-5638.
  • Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ et al: The effects of circumcision on the penis microbiome. PloS one 2010, 5(1):e8422.
  • Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y et al: Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics 2010, 42(12):1140-1143.
  • Foster JT, Allan GJ, Chan AP, Rabinowicz PD, Ravel J, Jackson PJ, Keim P: Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC plant biology 2010, 10:13.
  • Forney LJ, Gajer P, Williams CJ, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Brotman RM, Davis CC, Ault K et al: Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. Journal of clinical microbiology 2010, 48(5):1741-1748.
  • Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J: 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 2010, 192(6):1685-1699.
  • Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G et al: Draft genome sequence of the oilseed species Ricinus communis. Nature biotechnology 2010, 28(9):951-956.
  • Brotman RM, Ravel J, Cone RA, Zenilman JM: Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis. Sexually transmitted infections 2010, 86(4):297-302.


  • Simonson TS, Okinaka RT, Wang B, Easterday WR, Huynh L, U'Ren JM, Dukerich M, Zanecki SR, Kenefic LJ, Beaudry J et al: Bacillus anthracis in China and its relationship to worldwide lineages. BMC microbiology 2009, 9:71.
  • Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM et al: The complete genome sequence of Bacillus anthracis Ames "Ancestor". Journal of bacteriology 2009, 191(1):445-446.
  • Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, Bowers J, Rattray R, Ravel J, Kingsley C et al: Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PloS one 2009, 4(7):e6462.
  • Myers GS, Mathews SA, Eppinger M, Mitchell C, O'Brien KK, White OR, Benahmed F, Brunham RC, Read TD, Ravel J et al: Evidence that human Chlamydia pneumoniae was zoonotically acquired. Journal of bacteriology 2009, 191(23):7225-7233.
  • Kenefic LJ, Pearson T, Okinaka RT, Schupp JM, Wagner DM, Hoffmaster AR, Trim CB, Chung WK, Beaudry JA, Jiang L et al: Pre-Columbian origins for North American anthrax. PloS one 2009, 4(3):e4813.
  • Fricke WF, Welch TJ, McDermott PF, Mammel MK, LeClerc JE, White DG, Cebula TA, Ravel J: Comparative genomics of the IncA/C multidrug resistance plasmid family. Journal of bacteriology 2009, 191(15):4750-4757.
  • Fricke WF, Rasko DA, Ravel J: The role of genomics in the identification, prediction, and prevention of biological threats. PLoS biology 2009, 7(10):e1000217.
  • Fricke WF, McDermott PF, Mammel MK, Zhao S, Johnson TJ, Rasko DA, Fedorka-Cray PJ, Pedroso A, Whichard JM, Leclerc JE et al: Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry. Applied and environmental microbiology 2009, 75(18):5963-5971.
  • Eppinger M, Guo Z, Sebastian Y, Song Y, Lindler LE, Yang R, Ravel J: Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. Journal of bacteriology 2009, 191(24):7628-7629.
  • Bachmann BO, Ravel J: Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods in enzymology 2009, 458:181-217.


  • Wommack KE, Bhavsar J, Ravel J: Metagenomics: read length matters. Applied and environmental microbiology 2008, 74(5):1453-1463.
  • Schutzer SE, Schlater LR, Ronning CM, DeShazer D, Luft BJ, Dunn JJ, Ravel J, Fraser-Liggett CM, Nierman WC: Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists. PloS one 2008, 3(4):e2058.
  • Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R et al: The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of bacteriology 2008, 190(20):6881-6893.
  • Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R: Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. Journal of bacteriology 2008, 190(20):6779-6794.
  • Donia MS, Ravel J, Schmidt EW: A global assembly line for cyanobactins. Nature chemical biology 2008, 4(6):341-343.
  • Brotman RM, Ravel J: Ready or not: the molecular diagnosis of bacterial vaginosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2008, 47(1):44-46.


  • Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK, Eppinger M, Rosovitz MJ, Wagner D et al: Multiple antimicrobial resistance in plague: an emerging public health risk. PloS one 2007, 2(3):e309.
  • Van Ert MN, Easterday WR, Simonson TS, U'Ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB et al: Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of clinical microbiology 2007, 45(1):47-53.
  • Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U'Ren JM et al: Global genetic population structure of Bacillus anthracis. PloS one 2007, 2(5):e461.
  • Rasko DA, Rosovitz MJ, Okstad OA, Fouts DE, Jiang L, Cer RZ, Kolsto AB, Gill SR, Ravel J: 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 Bacillus anthracis pXO1. Journal of bacteriology 2007, 189(1):52-64.
  • Lee K, Costerton JW, Ravel J, Auerbach RK, Wagner DM, Keim P, Leid JG: Phenotypic and functional characterization of Bacillus anthracis biofilms. Microbiology (Reading, England) 2007, 153(Pt 6):1693-1701.
  • Eppinger M, Rosovitz MJ, Fricke WF, Rasko DA, Kokorina G, Fayolle C, Lindler LE, Carniel E, Ravel J: The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever. PLoS genetics 2007, 3(8):e142.
  • Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J et al: Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PloS one 2007, 2(8):e770.
  • Romero CM, DeShazer D, Feldblyum T, Ravel J, Woods D, Kim HS, Yu Y, Ronning CM, Nierman WC: Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts. BMC genomics 2006, 7:228.
  • Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM et al: Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome research 2006, 16(8):1031-1040.
  • Donia MS, Hathaway BJ, Sudek S, Haygood MG, Rosovitz MJ, Ravel J, Schmidt EW: Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nature chemical biology 2006, 2(12):729-735.
  • Dempsey MP, Nietfeldt J, Ravel J, Hinrichs S, Crawford R, Benson AK: Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp. tularensis and Francisella tularensis subsp. holarctica populations. Journal of bacteriology 2006, 188(16):5904-5914.
  • Zwick ME, McAfee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A: Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome biology 2005, 6(1):R10.
  • Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J: 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 of the United States of America 2005, 102(20):7315-7320.
  • Ravel J, Fraser CM: Genomics at the genus scale. Trends in microbiology 2005, 13(3):95-97.
  • Rasko DA, Myers GS, Ravel J: Visualization of comparative genomic analyses by BLAST score ratio. BMC bioinformatics 2005, 6:2.
  • Rasko DA, Altherr MR, Han CS, Ravel J: Genomics of the Bacillus cereus group of organisms. FEMS microbiology reviews 2005, 29(2):303-329.
  • Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R et al: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature biotechnology 2005, 23(7):873-878.
  • Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M et al: Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. Journal of bacteriology 2005, 187(7):2426-2438.
  • Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC et al: Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS biology 2005, 3(1):e15.
  • Budowle B, Schutzer SE, Ascher MS, Atlas RM, Burans JP, Chakraborty R, Dunn JJ, Fraser CM, Franz DR, Leighton TJ et al: Toward a system of microbial forensics: from sample collection to interpretation of evidence. Applied and environmental microbiology 2005, 71(5):2209-2213.
  • Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH et al: Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS biology 2004, 2(10):e303.
  • Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV et al: The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic acids research 2004, 32(3):977-988.
  • Pearson T, Busch JD, Ravel J, Read TD, Rhoton SD, U'Ren JM, Simonson TS, Kachur SM, Leadem RR, Cardon ML et al: Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(37):13536-13541.
  • Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT et al: Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids research 2004, 32(8):2386-2395.
  • Liu H, Bergman NH, Thomason B, Shallom S, Hazen A, Crossno J, Rasko DA, Ravel J, Read TD, Peterson SN et al: Formation and composition of the Bacillus anthracis endospore. Journal of bacteriology 2004, 186(1):164-178.
  • Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, De BK, Sacchi CT, Fitzgerald C, Mayer LW et al: Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(22):8449-8454.
  • Gunsior M, Ravel J, Challis GL, Townsend CA: Engineering p-hydroxyphenylpyruvate dioxygenase to a p-hydroxymandelate synthase and evidence for the proposed benzene oxide intermediate in homogentisate formation. Biochemistry 2004, 43(3):663-674.
  • Gunsior M, Breazeale SD, Lind AJ, Ravel J, Janc JW, Townsend CA: The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A. Chemistry & biology 2004, 11(7):927-938.
  • Baer ML, Ravel J, Pineiro SA, Guether-Borg D, Williams HN: Reclassification of salt-water Bdellovibrio sp. as Bacteriovorax marinus sp. nov. and Bacteriovorax litoralis sp. nov. International journal of systematic and evolutionary microbiology 2004, 54(Pt 4):1011-1016.
  • Ravel J, Cornelis P: Genomics of pyoverdine-mediated iron uptake in pseudomonads. Trends in microbiology 2003, 11(5):195-200.
  • Ramaiah N, Ravel J, Straube WL, Hill RT, Colwell RR: Entry of Vibrio harveyi and Vibrio fischeri into the viable but nonculturable state. Journal of applied microbiology 2002, 93(1):108-116.
  • Mossialos D, Ochsner U, Baysse C, Chablain P, Pirnay JP, Koedam N, Budzikiewicz H, Fernandez DU, Schafer M, Ravel J et al: Identification of new, conserved, non-ribosomal peptide synthetases from fluorescent pseudomonads involved in the biosynthesis of the siderophore pyoverdine. Molecular microbiology 2002, 45(6):1673-1685.
  • Ravel J, Wellington EM, Hill RT: Interspecific transfer of Streptomyces giant linear plasmids in sterile amended soil microcosms. Applied and environmental microbiology 2000, 66(2):529-534.
  • Ravel J, DiRuggiero J, Robb FT, Hill RT: Cloning and sequence analysis of the mercury resistance operon of Streptomyces sp. Strain CHR28 reveals a novel putative second regulatory gene. Journal of bacteriology 2000, 182(8):2345-2349.
  • Ramaiah N, Hill RT, Chun J, Ravel J, Matte MH, Straube WL, Colwell RR: Use of a chiA probe for detection of chitinase genes in bacteria from the Chesapeake Bay(1). FEMS microbiology ecology 2000, 34(1):63-71.
  • Ramaiah N, Chun J, Ravel J, Straube WL, Hill RT, Colwell RR: Detection of luciferase gene sequences in nonluminescent bacteria from the Chesapeake Bay. FEMS microbiology ecology 2000, 33(1):27-34.
  • Challis GL, Ravel J, Townsend CA: Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chemistry & biology 2000, 7(3):211-224.
  • Challis GL, Ravel J: Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS microbiology letters 2000, 187(2):111-114.
  • Baer ML, Ravel J, Chun J, Hill RT, Williams HN: A proposal for the reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively. International journal of systematic and evolutionary microbiology 2000, 50 Pt 1:219-224.
  • Wommack KE, Ravel J, Hill RT, Colwell RR: Hybridization analysis of chesapeake bay virioplankton. Applied and environmental microbiology 1999, 65(1):241-250.
  • Wommack KE, Ravel J, Hill RT, Chun J, Colwell RR: Population dynamics of chesapeake bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Applied and environmental microbiology 1999, 65(1):231-240.
  • Ravel J, Schrempf H, Hill RT: Mercury resistance is encoded by transferable giant linear plasmids in two chesapeake bay Streptomyces strains. Applied and environmental microbiology 1998, 64(9):3383-3388.
  • Ravel J, Amoroso MJ, Colwell RR, Hill RT: Mercury-resistant actinomycetes from the Chesapeake Bay. FEMS microbiology letters 1998, 162(1):177-184.
  • DiRuggiero J, Santangelo N, Nackerdien Z, Ravel J, Robb FT: Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of bacteriology 1997, 179(14):4643-4645.
  • Ravel J, Knight IT, Monahan CE, Hill RT, Colwell RR: Temperature-induced recovery of Vibrio cholerae from the viable but nonculturable state: growth or resuscitation? Microbiology (Reading, England) 1995, 141 ( Pt 2):377-383.
  • Ravel J, Hill RT, Colwell RR: Isolation of a Vibrio cholerae transposon-mutant with an altered viable but nonculturable response. FEMS microbiology letters 1994, 120(1-2):57-61.