Bacterial genomics

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List of sequenced bacterial genomes

 

External links

http://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes

 

Project pages and papers

  1.  "Entrez Genome Database Search". National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome. Search for details on specific genomes by organism name and strain.
  2. ^ Deckert G et al. (1998). "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus". Nature 392 (6674): 353–8. DOI:10.1038/32831. PMID 9537320.
  3. ^ Cerdeño-Tárraga AM et al. (2005). "Extensive DNA inversions in the B. fragilis genome control variable gene expression". Science 307 (5714): 1463–5. DOI:10.1126/science.1107008. PMID 15746427. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=15746427.
  4. ^ Kuwahara T, Yamashita A, Hirakawa H, et al. (2004). "Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation". PNAS 101 (41): 14919–14924.
  5. ^ Xu J et al. (2003). "A genomic view of the human-Bacteroides thetaiotaomicron symbiosis". Science 299 (5615): 2074–6. DOI:10.1126/science.1080029. PMID 12663928. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=12663928.
  6. ^ Schmitz-Esser,S., Tischler,P., Arnold,R., et al. (2010). "The genome of the amoeba symbiont 'Candidatus Amoebophilus asiaticus' reveals common mechanisms for host cell interaction among amoeba-associated bacteria". J. Bacteriol. 192 (4): 1045–1057. DOI:10.1128/JB.01379-09. PMC 2812958. PMID 20023027. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2812958.
  7. ^ Eisen JA et al. (2002). "The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium". Proc Natl Acad Sci U S 99 (14): 9509–14. DOI:10.1073/pnas.132181499. PMC 123171. PMID 12093901. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12093901.
  8. ^ Xie G, Bruce DC, Challacombe JF, et al. (June, 2007). "Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii". Appl Environ Microbiol. 73 (11): 3536–3546. DOI:10.1128/AEM.00225-07. PMC 1932680. PMID 17400776. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1932680.
  9. ^ Daligault,H., Lapidus,A., Zeytun,A., et al. (2011). "Complete genome sequence of Haliscomenobacter hydrossis type strain (O)". Stand Genomic Sci 4 (3): 352–360. DOI:10.4056/sigs.1964579. PMC 3156403. PMID 21886862. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3156403.
  10. ^ Naito M, Hirakawa H, Yamashita A, et al. (2008). "Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis". DNA Res. 15 (4): 215–225. DOI:10.1093/dnares/dsn013. PMC 2575886. PMID 18524787. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2575886.
  11. ^ Nelson KE et al. (2003). "Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83". J Bacteriol 185 (18): 5591–601. DOI:10.1128/JB.185.18.5591-5601.2003. PMC 193775. PMID 12949112. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=12949112.
  12. ^ Mongodin EF et al. (2005). "The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea". Proc Natl Acad Sci USA 102 (50): 18147–52. DOI:10.1073/pnas.0509073102. PMC 1312414. PMID 16330755. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16330755.
  13. ^ Pena A, Teeling H, Huerta-Cepas J, et al. (2010). "Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains". ISME J 4 (7): 882–895.
  14. ^ a b Read TD et al. (2000). "Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39". Nucleic Acids Res 28 (6): 1397–406. DOI:10.1093/nar/28.6.1397. PMC 111046. PMID 10684935. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10684935.
  15. ^ Carlson JH et al. (2005). "Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains". Infect Immun 73 (10): 6407–18. DOI:10.1128/IAI.73.10.6407-6418.2005. PMC 1230933. PMID 16177312. http://iai.asm.org/cgi/pmidlookup?view=long&pmid=16177312.
  16. ^ Stephens RS et al. (1998). "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis". Science 282 (5389): 754–9. DOI:10.1126/science.282.5389.754. PMID 9784136. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=9784136.
  17. ^ Thomson NR et al. (2005). "The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation". Genome Res 15 (5): 629–40. DOI:10.1101/gr.3684805. PMC 1088291. PMID 15837807. http://www.genome.org/cgi/pmidlookup?view=long&pmid=15837807.
  18. ^ Read TD et al. (2003). "Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae". Nucleic Acids Res 31 (8): 2134–47. DOI:10.1093/nar/gkg321. PMC 153749. PMID 12682364. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12682364.
  19. ^ Kalman S et al. (1999). "Comparative genomes of Chlamydia pneumoniae and C. trachomatis". Nat Genet 21 (4): 385–9. DOI:10.1038/7716. PMID 10192388.
  20. ^ J Infect Dis. 2000 Jun, 181 Suppl 3:S524-7
  21. ^ Horn M et al. (2004). "Illuminating the evolutionary history of chlamydiae". Science 304 (5671): 728–30. DOI:10.1126/science.1096330. PMID 15073324. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=15073324.
  22. ^ Seshadri R et al. (2005). "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes". Science 307 (5706): 105–8. DOI:10.1126/science.1102226. PMID 15637277. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=15637277.
  23. ^ Kube M et al. (2005). "Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1". Nat Biotechnol 23 (10): 1269–73. DOI:10.1038/nbt1131. PMID 16116419.
  24. ^ DNA Res. 2001 Oct 31;8(5):205-13, 8(5):205-13; 227-53
  25. ^ a b Allewalt JP et al. (2006). "Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the octopus spring microbial mat community of Yellowstone National Park". Appl Environ Microbiol 72 (1): 544–50. DOI:10.1128/AEM.72.1.544-550.2006. PMC 1352173. PMID 16391090. http://aem.asm.org/cgi/pmidlookup?view=long&pmid=16391090.
  26. ^ Nakamura Y et al. (2003). "Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids". DNA Res 10 (4): 137–45. DOI:10.1093/dnares/10.4.137. PMID 14621292. http://dnaresearch.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14621292.
  27. ^ a b Rocap G et al. (2003). "Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation". Nature 424 (6952): 1042–7. DOI:10.1038/nature01947. PMID 12917642.
  28. ^ Dufresne A et al. (2003). "Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome". Proc Natl Acad Sci USA 100 (17): 10020–5. DOI:10.1073/pnas.1733211100. PMC 187748. PMID 12917486. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12917486.
  29. ^ Palenik B et al. (2003). "The genome of a motile marine Synechococcus". Nature 424 (6952): 1037–42. DOI:10.1038/nature01943. PMID 12917641.
  30. ^ Kaneko, T. et al. (1995). "Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence Features in the 1 Mb Region from Map Positions 64% to 92% of the Genome". DNA Res. 2 (4): 153–66. DOI:10.1093/dnares/2.4.153. PMID 8590279.
  31. ^ de Groot A, Dulermo R, Ortet P, et al. (2009). "Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti". PLoS Genet. 5 (3): e1000434.
  32. ^ Yuan M, Chen M, Zhang W, et al. (2012). "Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis: Insights into the Extreme Environmental Adaptations". PLoS ONE 7 (3): e34458.
  33. ^ White O et al. (1999). "Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1". Science 286 (5444): 1571–7. DOI:10.1126/science.286.5444.1571. PMID 10567266. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=10567266.
  34. ^ Sikorski J, Tindall BJ, Lowry S, et al. (2010). "Complete genome sequence of Meiothermus silvanus type strain (VI-R2)". Stand Genomic Sci 3 (1): 37–46. DOI:10.4056/sigs.1042812. PMC 3035272. PMID 21304690. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035272.
  35. ^ Gounder K, Brzuszkiewicz E, Liesegang H, et al. (2011). "Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01". BMC Genomics 12: 577.
  36. ^ Henne A et al. (2004). "The genome sequence of the extreme thermophile Thermus thermophilus". Nat Biotechnol 22 (5): 547–53. DOI:10.1038/nbt956. PMID 15064768.
  37. ^ Schell MA et al. (2002). "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract". Proc Natl Acad Sci USA 99 (22): 14422–7. DOI:10.1073/pnas.212527599. PMC 137899. PMID 12381787. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12381787.
  38. ^ Cerde√ɬ±o-T√ɬ°rraga AM et al. (2003). "The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129". Nucleic Acids Res 31 (22): 6516–23. DOI:10.1093/nar/gkg874. PMC 275568. PMID 14602910. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14602910.
  39. ^ Nishio Y et al. (2003). "Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens". Genome Res 13 (7): 1572–9. DOI:10.1101/gr.1285603. PMC 403753. PMID 12840036. http://www.genome.org/cgi/pmidlookup?view=long&pmid=12840036.
  40. ^ Kalinowski J et al. (2003). "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins". J Biotechnol 104 (1–3): 5–25. DOI:10.1016/S0168-1656(03)00154-8. PMID 12948626. http://linkinghub.elsevier.com/retrieve/pii/S0168165603001548.
  41. ^ Tauch A et al. (2005). "Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora". J Bacteriol 187 (13): 4671–82. DOI:10.1128/JB.187.13.4671-4682.2005. PMC 1151758. PMID 15968079. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=15968079.
  42. ^ Li L et al. (2005). "The complete genome sequence of Mycobacterium avium subspecies paratuberculosis". Proc Natl Acad Sci USA 102 (35): 12344–9. DOI:10.1073/pnas.0505662102. PMC 1194940. PMID 16116077. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16116077.
  43. ^ Garnier T et al. (2003). "The complete genome sequence of Mycobacterium bovis". Proc Natl Acad Sci USA 100 (13): 7877–82. DOI:10.1073/pnas.1130426100. PMC 164681. PMID 12788972. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12788972.
  44. ^ Cole ST et al. (2001). "Massive gene decay in the leprosy bacillus". Nature 409 (6823): 1007–11. DOI:10.1038/35059006. PMID 11234002.
  45. ^ Cole ST et al. (1998). "Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence". Nature 393 (6685): 537–44. DOI:10.1038/31159. PMID 9634230.
  46. ^ Ishikawa J et al. (2004). "The complete genomic sequence of Nocardia farcinica IFM 10152". Proc Natl Acad Sci USA 101 (41): 14925–30. DOI:10.1073/pnas.0406410101. PMC 522048. PMID 15466710. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=15466710.
  47. ^ Omura S et al. (2001). "Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites". Proc Natl Acad Sci USA 98 (21): 12215–20. DOI:10.1073/pnas.211433198. PMC 59794. PMID 11572948. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=11572948.
  48. ^ Redenbach M et al. (1996). "A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome". Mol Microbiol 21 (1): 77–96. DOI:10.1046/j.1365-2958.1996.6191336.x. PMID 8843436.
  49. ^ Ueda K et al. (2004). "Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism". Nucleic Acids Res 32 (16): 4937–44. DOI:10.1093/nar/gkh830. PMC 519118. PMID 15383646. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15383646.
  50. ^ Raoult D et al. (2003). "Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome". Genome Res 13 (8): 1800–9. DOI:10.1101/gr.1474603 (inactive 2010-03-16). PMC 403771. PMID 12902375. http://www.genome.org/cgi/pmidlookup?view=long&pmid=12902375.
  51. ^ Read TD et al. (2003). "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria". Nature 423 (6935): 81–6. DOI:10.1038/nature01586. PMID 12721629.
  52. ^ Rasko DA et al. (2004). "The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1". Nucleic Acids Res 32 (3): 977–88. DOI:10.1093/nar/gkh258. PMC 373394. PMID 14960714. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14960714.
  53. ^ Ivanova N et al. (2003). "Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis". Nature 423 (6935): 87–91. DOI:10.1038/nature01582. PMID 12721630.
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  55. ^ Takami H et al. (1999). "An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125". Extremophiles 3 (1): 21–8. DOI:10.1007/s007920050095. PMID 10086841.
  56. ^ Rey MW et al. (2004). "Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species". Genome Biol 5 (10): R77. DOI:10.1186/gb-2004-5-10-r77. PMC 545597. PMID 15461803. http://genomebiology.com/1465-6906/5/R77.
  57. ^ a b Veith B et al. (2004). "The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential". J Mol Microbiol Biotechnol 7 (4): 204–11. DOI:10.1159/000079829. PMID 15383718. http://content.karger.com/produktedb/produkte.asp?doi=10.1159/000079829&typ=pdf.
  58. ^ Kunst F et al. (1997). "The complete genome sequence of the gram-positive bacterium Bacillus subtilis". Nature 390 (6657): 249–56. DOI:10.1038/36786. PMID 9384377.
  59. ^ Nölling J et al. (2001). "Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum". J Bacteriol 183 (16): 4823–38. DOI:10.1128/JB.183.16.4823-4838.2001. PMC 99537. PMID 11466286. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=11466286.
  60. ^ Shimizu T et al. (2002). "Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater". Proc Natl Acad Sci USA 99 (2): 996–1001. DOI:10.1073/pnas.022493799. PMC 117419. PMID 11792842. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=11792842.
  61. ^ Bruggemann H et al. (2003). "The genome sequence of Clostridium tetani, the causative agent of tetanus disease". Proc Natl Acad Sci USA 100 (3): 1316–21. DOI:10.1073/pnas.0335853100. PMC 298770. PMID 12552129. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12552129.
  62. ^ Nonaka H et al. (2006). "Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195". J Bacteriol 188 (6): 2262–74. DOI:10.1128/JB.188.6.2262-2274.2006. PMC 1428132. PMID 16513756. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=16513756.
  63. ^ Paulsen IT et al. (2003). "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis". Science 299 (5615): 2071–4. DOI:10.1126/science.1080613. PMID 12663927. http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=12663927.
  64. ^ Takami H et al. (2004). "Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus". Nucleic Acids Res 32 (21): 6292–303. DOI:10.1093/nar/gkh970. PMC 535678. PMID 15576355. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15576355.
  65. ^ Altermann E et al. (2005). "Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM". Proc Natl Acad Sci USA 102 (11): 3906–12. DOI:10.1073/pnas.0409188102. PMC 554803. PMID 15671160. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=15671160.
  66. ^ a b Pridmore RD et al. (2004). "The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533". Proc Natl Acad Sci USA 101 (8): 2512–7. DOI:10.1073/pnas.0307327101. PMC 356981. PMID 14983040. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=14983040.
  67. ^ Bolotin A et al. (2001). "The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403". Genome Res 11 (5): 731–53. DOI:10.1101/gr.169701. PMC 311110. PMID 11337471. http://www.genome.org/cgi/pmidlookup?view=long&pmid=11337471.
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  69. ^ Nelson KE et al. (2004). "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 Res 32 (8): 2386–95. DOI:10.1093/nar/gkh562. PMC 419451. PMID 15115801. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15115801.
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  81. ^ Ajdić D et al. (2002). "Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen". Proc Natl Acad Sci USA 99 (22): 14434–9. DOI:10.1073/pnas.172501299. PMC 137901. PMID 12397186. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12397186.
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