Jonathan A Eisen

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
    BMC Bioinformatics 13:264. 2012
  2. pmc Badomics words and the power and peril of the ome-meme
    Jonathan A Eisen
    Genome Center, University of California, Davis, CA, USA
    Gigascience 1:6. 2012
  3. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
  4. pmc Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
    Jorge Valdes
    Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile
    BMC Genomics 9:597. 2008
  5. pmc Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
    Jonathan A Eisen
    University of California Davis Genome Center, Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology, Davis, California, United States of America
    PLoS Biol 5:e82. 2007
  6. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
  7. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
  8. pmc Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 1:e65. 2005
  9. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
  10. pmc Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:5646-51. 2004

Detail Information

Publications61

  1. pmc Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
    BMC Bioinformatics 13:264. 2012
    ..We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences...
  2. pmc Badomics words and the power and peril of the ome-meme
    Jonathan A Eisen
    Genome Center, University of California, Davis, CA, USA
    Gigascience 1:6. 2012
    ..I focus on a bad aspect of this spread the use of what I refer to as "badomics" words. I discuss why these should be considered bad and how to distinguish badomics words from good ones...
  3. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
    ..Little is known about the mechanisms that enable this relationship...
  4. pmc Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
    Jorge Valdes
    Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile
    BMC Genomics 9:597. 2008
    ..Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism...
  5. pmc Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
    Jonathan A Eisen
    University of California Davis Genome Center, Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology, Davis, California, United States of America
    PLoS Biol 5:e82. 2007
  6. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...
  7. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  8. pmc Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 1:e65. 2005
    ....
  9. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
    ..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections...
  10. pmc Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:5646-51. 2004
    ....
  11. pmc The complete genome sequence of Haloferax volcanii DS2, a model archaeon
    Amber L Hartman
    Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9605. 2010
    ..This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general...
  12. pmc The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
    Douglas B Rusch
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e77. 2007
    ..Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS...
  13. ncbi Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
    Rekha Seshadri
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:105-8. 2005
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...
  14. pmc 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...
  15. ncbi Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
    ....
  16. ncbi The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  17. pmc Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum
    Dongying Wu
    University of California Davis Genome Center, Davis, California, USA
    PLoS ONE 4:e4207. 2009
    ..Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced...
  18. pmc Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
    Robert S Coyne
    J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
    BMC Genomics 9:562. 2008
    ....
  19. pmc Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
    Dongying Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 4:e188. 2006
    ..coagulata and other sharpshooters serve as vectors of transmission...
  20. ncbi Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales
    Jonathan H Badger
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Int J Syst Evol Microbiol 55:1021-6. 2005
    ..The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed...
  21. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
    ..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease...
  22. pmc Comparative genomics of emerging human ehrlichiosis agents
    Julie C Dunning Hotopp
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Genet 2:e21. 2006
    ..These discoveries provide significant insights into the biology of these obligate intracellular pathogens...
  23. pmc Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees
    Dongying Wu
    Department of Evolution and Ecology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 6:e18011. 2011
    ..Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species...
  24. pmc Complete genome sequence of the Q-fever pathogen Coxiella burnetii
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:5455-60. 2003
    ..burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation...
  25. ncbi The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 22:554-9. 2004
    ....
  26. ncbi Phylogenomics: intersection of evolution and genomics
    Jonathan A Eisen
    Institute for Genomic Research, Rockville, MD 20850, USA
    Science 300:1706-7. 2003
    ..Much has been gained from genomic and evolutionary studies of species. Combining the perspectives of these different approaches suggests that an integrated phylogenomic approach will be beneficial...
  27. pmc The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    Ian T Paulsen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:13148-53. 2002
    ..A limited repertoire of genes homologous to known bacterial virulence factors were identified...
  28. pmc Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts
    Kevin Penn
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Appl Environ Microbiol 72:1680-3. 2006
    ..More sampling is needed to understand the basis and significance of this variation...
  29. pmc Assembling the marine metagenome, one cell at a time
    Tanja Woyke
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e5299. 2009
    ..A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa...
  30. pmc Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts
    James Angus Chandler
    Department of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, USA
    Appl Environ Microbiol 78:7327-36. 2012
    ..Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach...
  31. pmc An integrated pipeline for de novo assembly of microbial genomes
    Andrew Tritt
    Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 7:e42304. 2012
    ..Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage...
  32. pmc An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP)
    Dongying Wu
    UC Davis Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 3:e2566. 2008
    ..Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts...
  33. pmc Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences
    Amber L Hartman
    Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    BMC Bioinformatics 11:317. 2010
    ..As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly...
  34. pmc A simple, fast, and accurate method of phylogenomic inference
    Martin Wu
    Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 9:R151. 2008
    ....
  35. pmc Drivers of bacterial beta-diversity depend on spatial scale
    Jennifer B H Martiny
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 108:7850-4. 2011
    ..These results highlight the importance of considering multiple spatial scales for understanding microbial biogeography...
  36. ncbi The age of the Arabidopsis thaliana genome duplication
    Maria D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant Mol Biol 51:859-66. 2003
    ..In each case, our estimate places the age of the genome duplication as significantly younger than previously reported...
  37. pmc Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae
    Herve Tettelin
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:12391-6. 2002
    ..agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms...
  38. pmc The value of complete microbial genome sequencing (you get what you pay for)
    Claire M Fraser
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:6403-5; discusion 6405. 2002
  39. ncbi Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  40. pmc BioTorrents: a file sharing service for scientific data
    Morgan G I Langille
    Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 5:e10071. 2010
    ..BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net...
  41. pmc Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)
    Zachary A Bendiks
    University of California at Davis, Genome Center, Davis, California, USA
    Genome Announc 1:e0012013. 2013
    ..The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment...
  42. pmc The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e16. 2007
    ..Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature...
  43. pmc Mauve assembly metrics
    Aaron E Darling
    Genome Center, University of California Davis, Davis, CA 95616, USA
    Bioinformatics 27:2756-7. 2011
    ....
  44. pmc Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system
    James Angus Chandler
    Center for Population Biology, Department of Evolution and Ecology, University of California Davis, Davis, California, USA
    PLoS Genet 7:e1002272. 2011
    ..Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab...
  45. pmc New evolutionary frontiers from unusual virus genomes
    Christopher Desjardins
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20854, USA
    Genome Biol 6:212. 2005
    ..These and other unusual features challenge the way we view the evolution and definition of viruses...
  46. pmc PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 7:e1001061. 2011
    ..Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?..
  47. pmc Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices
    Jenna Morgan Lang
    Department of Medical Microbiology and Immunology and Department of Evolution and Ecology, University of California Davis, Davis, California, USA
    PLoS ONE 8:e62510. 2013
    ....
  48. ncbi Phylogenetic analysis and gene functional predictions: phylogenomics in action
    Jonathan A Eisen
    Department of Microbial Genomics, The Instiute for Genomic Research, Rockville, Maryland 20850, USA
    Theor Popul Biol 61:481-7. 2002
    ..Examples that are discussed include phylogenetic determination of orthology, the use of character state reconstruction analysis of gene function, and evolutionary analysis of rates and patterns of gene evolution...
  49. pmc The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
    Jonathan A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:9509-14. 2002
    ..tepidum and many Archaeal species...
  50. doi Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
    Cindy J Castelle
    Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
    Nat Commun 4:2120. 2013
    ..We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations. ..
  51. pmc Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4
    Jonathon R Lo
    University of California at Davis, Genome Center, Davis, California, USA
    Genome Announc 1:e0008613. 2013
    ..The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7% identical to that of the original B. muris strain, C3H-21...
  52. pmc Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome
    Eileen P Hamilton
    Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
    Genomics 88:443-51. 2006
    ....
  53. pmc Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis
    David Alland
    Department of Medicine, Center for Emerging Pathogens, New Jersey Medical School, Newark, New Jersey 07103, USA
    J Bacteriol 185:3392-9. 2003
    ..Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure...
  54. pmc Identification of a fourth family of lycopene cyclases in photosynthetic bacteria
    Julia A Maresca
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:11784-9. 2007
    ..Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria...
  55. ncbi Brouhaha over the other yeast
    Jonathan A Eisen
    Nature 415:845-8. 2002
  56. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...
  57. pmc A cut above: discovery of an alternative excision repair pathway in bacteria
    Bennett Van Houten
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 99:2581-3. 2002
  58. ncbi Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
    Mary Ann Moran
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Nature 432:910-3. 2004
    ..This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean...
  59. ncbi Comparative studies of resistin expression and phylogenomics in human and mouse
    Rong Ze Yang
    Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
    Biochem Biophys Res Commun 310:927-35. 2003
    ..The high expression of resistin in human leukemia cells suggests a hitherto unidentified biological function of resistin in leukocytes...
  60. ncbi Unsuspected diversity among marine aerobic anoxygenic phototrophs
    Oded Beja
    Monterey Bay Aquarium Research Institute, Moss Landing, California 95039 0628, USA
    Nature 415:630-3. 2002
    ....
  61. pmc Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp
    Tracy H Hazen
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Appl Environ Microbiol 73:7703-10. 2007
    ..This study provides evidence of genetic exchange between Vibrio plasmids, phages, and chromosomes among diverse Vibrio spp...