Jacques Ravel

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. ncbi Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
  2. ncbi Whole-genome sequences of Bacillus subtilis and close relatives
    Ashlee M Earl
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, USA
    J Bacteriol 194:2378-9. 2012
  3. ncbi Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    BMC Plant Biol 10:13. 2010
  4. ncbi Bacillus anthracis in China and its relationship to worldwide lineages
    Tatum S Simonson
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    BMC Microbiol 9:71. 2009
  5. ncbi Vaginal microbiome of reproductive-age women
    Jacques Ravel
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:4680-7. 2011
  6. ncbi The complete genome sequence of Bacillus anthracis Ames "Ancestor"
    Jacques Ravel
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 191:445-6. 2009
  7. ncbi 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
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 189:52-64. 2007
  8. ncbi Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
    W Florian Fricke
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 190:6779-94. 2008
  9. ncbi Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women
    Rebecca M Brotman
    Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Sex Transm Dis 39:807-12. 2012
  10. ncbi Genomic anatomy of Escherichia coli O157:H7 outbreaks
    Mark Eppinger
    Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:20142-7. 2011

Detail Information

Publications46

  1. ncbi Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
    ..Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints...
  2. ncbi Whole-genome sequences of Bacillus subtilis and close relatives
    Ashlee M Earl
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, USA
    J Bacteriol 194:2378-9. 2012
    ..We report the high-quality Sanger genome sequences of B. subtilis subspecies subtilis RO-NN-1 and AUSI98, B. subtilis subspecies spizizenii TU-B-10(T) and DV1-B-1, Bacillus mojavensis RO-H-1(T), and Bacillus vallismortis DV1-F-3(T)...
  3. ncbi Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    BMC Plant Biol 10:13. 2010
    ..We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci...
  4. ncbi Bacillus anthracis in China and its relationship to worldwide lineages
    Tatum S Simonson
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    BMC Microbiol 9:71. 2009
    ..Canonical single nucleotide polymorphism (canSNP) and multiple locus VNTR analysis (MLVA) typing has been used to examine this archival collection of isolates...
  5. ncbi Vaginal microbiome of reproductive-age women
    Jacques Ravel
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:4680-7. 2011
    ....
  6. ncbi The complete genome sequence of Bacillus anthracis Ames "Ancestor"
    Jacques Ravel
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 191:445-6. 2009
    ..This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981...
  7. ncbi 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
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 189:52-64. 2007
    ..This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species...
  8. ncbi Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
    W Florian Fricke
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 190:6779-94. 2008
    ..The association of antimicrobial resistance with APEC virulence genes on pSMS35_130 highlights the risk of promoting the spread of virulence through the extensive use of antibiotics...
  9. ncbi Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women
    Rebecca M Brotman
    Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Sex Transm Dis 39:807-12. 2012
    ..We sought to evaluate the relationship between vaginal bacterial composition and Trichomonas vaginalis...
  10. ncbi Genomic anatomy of Escherichia coli O157:H7 outbreaks
    Mark Eppinger
    Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:20142-7. 2011
    ..coli O157:H7 resistance and virulence phenotypes...
  11. ncbi 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
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
    ..Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis...
  12. ncbi Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry
    W Florian Fricke
    Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore St, Baltimore, MD 21201, USA
    Appl Environ Microbiol 75:5963-71. 2009
    ....
  13. ncbi The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
    J Bacteriol 190:6881-93. 2008
    ..This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens...
  14. ncbi Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution
    W Florian Fricke
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 193:3556-68. 2011
    ..CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks...
  15. ncbi Comparative genomics of the IncA/C multidrug resistance plasmid family
    W Florian Fricke
    Institute for Genome Sciences IGS, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    J Bacteriol 191:4750-7. 2009
    ....
  16. ncbi Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5
    Ian T Paulsen
    The Institute for Genomic Research, Rockville, Maryland, USA
    Nat Biotechnol 23:873-8. 2005
    ..In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5...
  17. ncbi Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
    Derrick E Fouts
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 3:e15. 2005
    ....
  18. ncbi Temporal dynamics of the human vaginal microbiota
    Pawel Gajer
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Sci Transl Med 4:132ra52. 2012
    ..The women studied are healthy; thus, it appears that neither variation in community composition per se nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis...
  19. ncbi Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium
    Mark Eppinger
    Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, USA
    J Bacteriol 192:1685-99. 2010
    ..These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies...
  20. ncbi Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China
    Mark Eppinger
    Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, MD, USA
    J Bacteriol 191:7628-9. 2009
    ..These resources enable in-depth studies of Y. pestis sequence variations and detailed whole-genome comparisons of very closely related genomes from the supposed site of the origin and the emergence of global pandemics of plague...
  21. ncbi Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319
    Mark Eppinger
    Institute for Genomic Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
    J Bacteriol 193:4199-213. 2011
    ..This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle...
  22. ncbi 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
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
    ..Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs...
  23. ncbi The role of genomics in the identification, prediction, and prevention of biological threats
    W Florian Fricke
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
    PLoS Biol 7:e1000217. 2009
    ....
  24. ncbi Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:5027-32. 2011
    ..This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics...
  25. ncbi Comparison of storage conditions for human vaginal microbiome studies
    Guoyun Bai
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 7:e36934. 2012
    ..We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and (1)H-NMR analyses...
  26. ncbi Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir
    Mark Eppinger
    Institute for Genome Sciences IGS, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
    Appl Environ Microbiol 77:2916-25. 2011
    ..The presented extended list of polymorphic markers is valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies of this emerging human pathogen...
  27. ncbi Genomics of the Bacillus cereus group of organisms
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    FEMS Microbiol Rev 29:303-29. 2005
    ..Genomic data have spurred functional studies that combined microarrays and proteomics. Recent advances are reviewed in this article and highlight the advantages of genomic approaches to the study of this important group of bacteria...
  28. ncbi Castor bean organelle genome sequencing and worldwide genetic diversity analysis
    Maximo Rivarola
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e21743. 2011
    ....
  29. ncbi Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study
    Roberto Flores
    Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Rockville, MD 20852, USA
    J Transl Med 10:253. 2012
    ..Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identify members and functions of the intestinal microbial community associated with estrogen levels via enterohepatic recirculation...
  30. ncbi Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities
    Roberto Flores
    Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
    Eur J Clin Invest 42:848-54. 2012
    ..To facilitate epidemiologic and clinical research, we sought to optimize conditions and to assess reproducibility of selected core functions of the distal gut microbiota, β-glucuronidase and β-glucosidase bioactivities...
  31. ncbi The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:977-88. 2004
    ..The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk...
  32. ncbi Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants
    Maria Sellitto
    Mucosal Biology Research Center and Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 7:e33387. 2012
    ..This study constitutes a definite proof-of-principle that these combined genomic and metabolomic approaches will be key to deciphering the role of the gut microbiota on CD onset...
  33. ncbi Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray
    Michael C Schatz
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    Appl Environ Microbiol 76:5636-8. 2010
    ..PhyloTrac is free for noncommercial organizations and is available for all major operating systems at http://www.phylotrac.org/...
  34. ncbi Visualization of comparative genomic analyses by BLAST score ratio
    David A Rasko
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 6:2. 2005
    ..This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis...
  35. ncbi Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
    Garry S A Myers
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 16:1031-40. 2006
    ....
  36. ncbi Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts
    Claudia M Romero
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 7:228. 2006
    ..mallei ATCC 23344 isolates, one from each source, were sequenced from culture, a mouse, a horse, and two isolates from a single human patient, and the sequence compared to the published B. mallei ATCC 23344 genome sequence...
  37. ncbi Genomics at the genus scale
    Jacques Ravel
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Trends Microbiol 13:95-7. 2005
  38. ncbi Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
    Naomi Ward
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:e303. 2004
    ..We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential...
  39. ncbi Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences
    Roberto Flores
    Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
    Eur J Clin Invest 42:855-63. 2012
    ..We conducted a pilot study of reproducibility and associations of microbial diversity and composition in faecal microbial DNA...
  40. ncbi Vaginal microbiome: rethinking health and disease
    Bing Ma
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201, USA
    Annu Rev Microbiol 66:371-89. 2012
    ....
  41. ncbi Draft genome sequence of the oilseed species Ricinus communis
    Agnes P Chan
    J Craig Venter Institute, Rockville, Maryland, USA
    Nat Biotechnol 28:951-6. 2010
    ..Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage...
  42. ncbi Reclassification of salt-water Bdellovibrio sp. as Bacteriovorax marinus sp. nov. and Bacteriovorax litoralis sp. nov
    Marcie L Baer
    Department of Biomedical Sciences, University of Maryland at Baltimore, 666 W Baltimore Street, Baltimore, MD 21201, USA
    Int J Syst Evol Microbiol 54:1011-6. 2004
    ..nov. and Bacteriovorax litoralis sp. nov., respectively...
  43. ncbi The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A
    Michele Gunsior
    Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    Chem Biol 11:927-38. 2004
    ..Several enzymes involved in antibiotic biosynthesis were heterologously overproduced, and biochemical characterization confirmed their proposed activities...
  44. ncbi Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis
    Rebecca M Brotman
    Department of Epidemiology and Preventive Medicine, Institute for Genome Sciences, University of Maryland School of Medicine, BioPark Building II, 801 West Baltimore Street, Baltimore, MD 21201, USA
    Sex Transm Infect 86:297-302. 2010
    ..The aetiology of bacterial vaginosis (BV) remains unknown...
  45. ncbi Genome sequence of Ruegeria sp. strain KLH11, an N-acylhomoserine lactone-producing bacterium isolated from the marine sponge Mycale laxissima
    Jindong Zan
    Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center Suite 236, 701 East Pratt Street, Baltimore, MD 21202, USA
    J Bacteriol 193:5011-2. 2011
    ..The genome sequence provides insights into the genetic potential of KLH11 to maintain complex QS systems, and this is the first genome report of a cultivated symbiont from a marine sponge...
  46. ncbi Genomics of pyoverdine-mediated iron uptake in pseudomonads
    Jacques Ravel
    The Institute for Genomics Research, Pathogen Functional Genomics Resource Center, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Trends Microbiol 11:195-200. 2003
    ..Regulation of PVD production and uptake depends on two extracytoplasmic sigma factors (ECF-sigmas), PvdS and FpvI, together with one anti-sigma, FpvR...