Skip to main content
NCBI home page
Emerging Infectious Diseases logoLink to Emerging Infectious Diseases
. 2000 Sep-Oct;6(5):505–512. doi: 10.3201/eid0605.000510

Comparative genomics and understanding of microbial biology.

C M Fraser 1, J Eisen 1, R D Fleischmann 1, K A Ketchum 1, S Peterson 1
PMCID: PMC2627966  PMID: 10998382

Abstract

The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.

Full Text

The Full Text of this article is available as a PDF (85.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alm R. A., Ling L. S., Moir D. T., King B. L., Brown E. D., Doig P. C., Smith D. R., Noonan B., Guild B. C., deJonge B. L. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 1999 Jan 14;397(6715):176–180. doi: 10.1038/16495. [DOI] [PubMed] [Google Scholar]
  2. Andersson S. G., Zomorodipour A., Andersson J. O., Sicheritz-Pontén T., Alsmark U. C., Podowski R. M., Näslund A. K., Eriksson A. S., Winkler H. H., Kurland C. G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 1998 Nov 12;396(6707):133–140. doi: 10.1038/24094. [DOI] [PubMed] [Google Scholar]
  3. Blattner F. R., Plunkett G., 3rd, Bloch C. A., Perna N. T., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K., Mayhew G. F. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  4. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  5. Casjens S., Palmer N., van Vugt R., Huang W. M., Stevenson B., Rosa P., Lathigra R., Sutton G., Peterson J., Dodson R. J. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol Microbiol. 2000 Feb;35(3):490–516. doi: 10.1046/j.1365-2958.2000.01698.x. [DOI] [PubMed] [Google Scholar]
  6. Deckert G., Warren P. V., Gaasterland T., Young W. G., Lenox A. L., Graham D. E., Overbeek R., Snead M. A., Keller M., Aujay M. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 1998 Mar 26;392(6674):353–358. doi: 10.1038/32831. [DOI] [PubMed] [Google Scholar]
  7. Eisen J. A. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 1998 Sep 15;26(18):4291–4300. doi: 10.1093/nar/26.18.4291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Eisen J. A. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 1998 Mar;8(3):163–167. doi: 10.1101/gr.8.3.163. [DOI] [PubMed] [Google Scholar]
  9. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  10. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. doi: 10.1126/science.270.5235.397. [DOI] [PubMed] [Google Scholar]
  11. Galtier N., Tourasse N., Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Science. 1999 Jan 8;283(5399):220–221. doi: 10.1126/science.283.5399.220. [DOI] [PubMed] [Google Scholar]
  12. Gardner M. J., Tettelin H., Carucci D. J., Cummings L. M., Aravind L., Koonin E. V., Shallom S., Mason T., Yu K., Fujii C. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science. 1998 Nov 6;282(5391):1126–1132. doi: 10.1126/science.282.5391.1126. [DOI] [PubMed] [Google Scholar]
  13. Hirt R. P., Logsdon J. M., Jr, Healy B., Dorey M. W., Doolittle W. F., Embley T. M. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):580–585. doi: 10.1073/pnas.96.2.580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R. W., Olinger L., Grimwood J., Davis R. W., Stephens R. S. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet. 1999 Apr;21(4):385–389. doi: 10.1038/7716. [DOI] [PubMed] [Google Scholar]
  15. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996 Jun 30;3(3):109–136. doi: 10.1093/dnares/3.3.109. [DOI] [PubMed] [Google Scholar]
  16. Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 1999 Apr 30;6(2):83-101, 145-52. doi: 10.1093/dnares/6.2.83. [DOI] [PubMed] [Google Scholar]
  17. Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 1998 Apr 30;5(2):55–76. doi: 10.1093/dnares/5.2.55. [DOI] [PubMed] [Google Scholar]
  18. Kunst F., Ogasawara N., Moszer I., Albertini A. M., Alloni G., Azevedo V., Bertero M. G., Bessières P., Bolotin A., Borchert S. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997 Nov 20;390(6657):249–256. doi: 10.1038/36786. [DOI] [PubMed] [Google Scholar]
  19. Lawrence J. G., Ochman H. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9413–9417. doi: 10.1073/pnas.95.16.9413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Manca C., Tsenova L., Barry C. E., 3rd, Bergtold A., Freeman S., Haslett P. A., Musser J. M., Freedman V. H., Kaplan G. Mycobacterium tuberculosis CDC1551 induces a more vigorous host response in vivo and in vitro, but is not more virulent than other clinical isolates. J Immunol. 1999 Jun 1;162(11):6740–6746. [PubMed] [Google Scholar]
  21. Myler P. J., Audleman L., deVos T., Hixson G., Kiser P., Lemley C., Magness C., Rickel E., Sisk E., Sunkin S. Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2902–2906. doi: 10.1073/pnas.96.6.2902. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Parkhill J., Wren B. W., Mungall K., Ketley J. M., Churcher C., Basham D., Chillingworth T., Davies R. M., Feltwell T., Holroyd S. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000 Feb 10;403(6770):665–668. doi: 10.1038/35001088. [DOI] [PubMed] [Google Scholar]
  23. Pellegrini M., Marcotte E. M., Thompson M. J., Eisenberg D., Yeates T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285–4288. doi: 10.1073/pnas.96.8.4285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Peterson S. N., Bailey C. C., Jensen J. S., Borre M. B., King E. S., Bott K. F., Hutchison C. A., 3rd Characterization of repetitive DNA in the Mycoplasma genitalium genome: possible role in the generation of antigenic variation. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11829–11833. doi: 10.1073/pnas.92.25.11829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Razin S. Molecular biology and genetics of mycoplasmas (Mollicutes). Microbiol Rev. 1985 Dec;49(4):419–455. doi: 10.1128/mr.49.4.419-455.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Read T. D., Brunham R. C., Shen C., Gill S. R., Heidelberg J. F., White O., Hickey E. K., Peterson J., Utterback T., Berry K. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 2000 Mar 15;28(6):1397–1406. doi: 10.1093/nar/28.6.1397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Smith D. R., Doucette-Stamm L. A., Deloughery C., Lee H., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol. 1997 Nov;179(22):7135–7155. doi: 10.1128/jb.179.22.7135-7155.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Stephens R. S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R. L., Zhao Q. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 1998 Oct 23;282(5389):754–759. doi: 10.1126/science.282.5389.754. [DOI] [PubMed] [Google Scholar]
  29. Tatusov R. L., Koonin E. V., Lipman D. J. A genomic perspective on protein families. Science. 1997 Oct 24;278(5338):631–637. doi: 10.1126/science.278.5338.631. [DOI] [PubMed] [Google Scholar]
  30. Tettelin H., Saunders N. J., Heidelberg J., Jeffries A. C., Nelson K. E., Eisen J. A., Ketchum K. A., Hood D. W., Peden J. F., Dodson R. J. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000 Mar 10;287(5459):1809–1815. doi: 10.1126/science.287.5459.1809. [DOI] [PubMed] [Google Scholar]
  31. White O., Eisen J. A., Heidelberg J. F., Hickey E. K., Peterson J. D., Dodson R. J., Haft D. H., Gwinn M. L., Nelson W. C., Richardson D. L. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 1999 Nov 19;286(5444):1571–1577. doi: 10.1126/science.286.5444.1571. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Emerging Infectious Diseases are provided here courtesy of Centers for Disease Control and Prevention

RESOURCES