Archaeal genomics

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List of sequenced archaeal genomes

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

 

Project pages and papers

  1. ^ Mardanov AV, Svetlitchnyi VA, Beletsky AV, et al. (August, 2010). "The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs". Appl Environ Microbiol. 76 (16): 5652–5657. DOI:10.1128/AEM.00599-10. PMC2918975. PMID20581186. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2918975.
  2. ^ Kawarabayasi, Y.; Hino, Y; Horikawa, H; Yamazaki, S; Haikawa, Y; Jin-No, K; Takahashi, M; Sekine, M et al. (1999). "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1". DNA Research 6 (2): 83–101, 145–52. DOI:10.1093/dnares/6.2.83. PMID10382966.
  3. ^ Ravin NV, Mardanov AV, Beletsky AV, et al. (April 2009). "Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis". J Bacteriology 191 (7): 2371–2379. DOI:10.1128/JB.01525-08. PMC2655497. PMID19114480. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2655497.
  4. ^ Brügger K, Chen L, Stark M, et al.' (May 2007). "The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C". Archaea 2 (2): 127–35. PMC2686385. PMID17350933. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2686385.
  5. ^ Podar M, Anderson I, Makarova KS, et al. (2008). "A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans". Genome Biol. 9 (11): R158. DOI:10.1186/gb-2008-9-11-r158. PMC2614490. PMID19000309. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2614490.
  6. ^ Göker M, Held B, Lapidus A, et al. (August 20, 2010). "Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1)". Stand Genomic Sci. 3 (1): 66–75. DOI:10.4056/sigs.1072907. PMC3035270. PMID21304693. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035270.
  7. ^ Anderson I, Göker M, Nolan M, et al. (July 1, 2011). "Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A)". Stand Genomic Sci. 4 (3): 381–392. DOI:10.4056/sigs.2014648. PMC3156397. PMID21886865. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3156397.
  8. ^ Anderson I, Wirth R, Lucas S, et al. (October 15, 2011). "Complete genome sequence of Staphylothermus hellenicus P8". Stand Genomic Sci. 5 (1): 12–20. DOI:10.4056/sigs.2054696. PMC3236042. PMID22180806. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3236042.
  9. ^ Anderson IJ, Dharmarajan L, Rodriguez J, et al. (April 2, 2009). "The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota". BMC Genomics 10: 145. DOI:10.1186/1471-2164-10-145. PMC2678158. PMID19341479. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2678158.
  10. ^ Spring S, Rachel R, Lapidus A, et al. (June 15, 2010). "Complete genome sequence of Thermosphaera aggregans type strain (M11TL)". Stand Genomic Sci. 2 (3): 245–259. DOI:10.4056/sigs.821804. PMC3035292. PMID21304709. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035292.
  11. ^ Extremophiles in press.
  12. ^ Liu LJ, You XY, Zheng H, et al. (July 2011). "Complete genome sequence of Metallosphaera cuprina, a metal sulfide-oxidizing archaeon from a hot spring". J. Bacteriol. 193 (13): 3387-33888. DOI:10.1128/JB.05038-11. PMC3133273. PMID21551305. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3133273.
  13. ^ Auernik KS, Maezato Y, Blum PH, Kelly RM (February 2008). "The genome sequence of the metal-mobilizing, extremely thermoacidophilic archaeon Metallosphaera sedula provides insights into bioleaching-associated metabolism". Appl Environ Microbiol. 74 (3): 682–692. DOI:10.1128/AEM.02019-07. PMC2227735. PMID18083856. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2227735.
  14. ^ Chen, L.; Brugger, K.; Skovgaard, M.; Redder, P.; She, Q.; Torarinsson, E.; Greve, B.; Awayez, M. et al. (2005). "The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota". J. Bacteriol. 187 (14): 4992–9. DOI:10.1128/JB.187.14.4992-4999.2005. PMC1169522. PMID15995215. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1169522.
  15. ^ a b Guo L, Brügger K, Liu C, et al. (Apr 2011). "Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies". J. Bacteriol. 193 (7): 1672–1680. DOI:10.1128/JB.01487-10. PMC3067641. PMID21278296. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3067641.
  16. ^ a b c d e f g Reno ML, Held NL, Fields CJ, et al. (May 26, 2009). "Biogeography of the Sulfolobus islandicus' pan-genome". PNAS 106 (21): 8605–8610. DOI:10.1073/pnas.0808945106. PMC2689034. PMID19435847. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2689034.
  17. ^ She Q, Singh RK, Confalonieri F, et al. (July 3, 2001). "The complete genome of the crenarchaeon Sulfolobus solfataricus P2". PNAS 98 (14): 7835–7840. DOI:10.1073/pnas.141222098. PMC35428. PMID11427726. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=35428.
  18. ^ Kawarabayasi, Y.; Hino, Y; Horikawa, H; Jin-No, K; Takahashi, M; Sekine, M; Baba, S; Ankai, A et al. (2001). "Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon, Sulfolobus tokodaii strain7". DNA Research 8 (4): 123–40. DOI:10.1093/dnares/8.4.123. PMID11572479.
  19. ^ Fitz-Gibbon, S. T.; Ladner, H; Kim, UJ; Stetter, KO; Simon, MI; Miller, JH (2002). "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum". Proceedings of the National Academy of Sciences 99 (2): 984–9. DOI:10.1073/pnas.241636498. PMC117417. PMID11792869. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=117417.
  20. ^ a b c d e "GOLD". http://www.genomesonline.org.
  21. ^ Anderson I, Rodriguez J, Susanti D, et al. (April 2008). "Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction". J. Bacteriol. 190 (8): 2957–2965. DOI:10.1128/JB.01949-07. PMC2293246. PMID18263724. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2293246.
  22. ^ Siebers B, Zaparty M, Raddatz G, et al. (2011). "The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota". PLoS ONE 6 (10): e24222. DOI:10.1371/journal.pone.0024222. PMID22003381.
  23. ^ Mardanov AV, Gumerov VM, Beletsky AV, et al. (June 2011). "Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20". J. Bacteriol. 193 (12): 3156–3157. DOI:10.1128/JB.00409-11. PMC3133184. PMID21478349. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3133184.
  24. ^ Mavromatis K, Sikorski J, Pabst E, et al. (September 28, 2010). "Complete genome sequence of Vulcanisaeta distributa type strain (IC-017)". Stand Genomic Sci. 3 (2): 117–125. DOI:10.4056/sigs.1113067. PMC3035369. PMID21304741. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035369.
  25. ^ Gumerov VM, Mardanov AV, Beletsky AV, et al. (May 2011). "Complete genome sequence of "Vulcanisaeta moutnovskia" strain 768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta". J. Bacteriol. 193 (9): 2355–2356. DOI:10.1128/JB.00237-11. PMC3133093. PMID21398550. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3133093.
  26. ^ Venter, J. Craig; Klenk, Hans-Peter; Clayton, Rebecca A.; Tomb, Jean-Francois; White, Owen; Nelson, Karen E.; Ketchum, Karen A.; Dodson, Robert J. et al. (1997). "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus". Nature 390 (6658): 364–70. DOI:10.1038/37052. PMID9389475.
  27. ^ von Jan M, Lapidus A, Del Rio TG, et al. (June 15, 2010). "Complete genome sequence of Archaeoglobus profundus type strain (AV18)". Stand Genomic Sci. 2 (3,): 327–346. DOI:10.4056/sigs.942153. PMC3035285. PMID21304717. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035285.
  28. ^ Anderson I, Risso C, Holmes D, et al. (October 15, 2011). "Complete genome sequence of 'Ferroglobus placidus AEDII12DO". Stand Genomic Sci. 5 (1): 50–60. DOI:10.4056/sigs.2225018. PMC3236036. PMID22180810. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3236036.
  29. ^ Roh SW, Nam YD, Nam SH, et al. (September, 2010). "Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon". J Bacteriol. 192 (17): 4528–4529. DOI:10.1128/JB.00663-10. PMC2937367. PMID20601480. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2937367.
  30. ^ Liu H, Wu Z, Li M, et al. (November 2011). "Complete genome sequence of Haloarcula hispanica, a Model Haloarchaeon for studying genetics, metabolism, and virus-host interaction". J. Bacteriol. 193 (21): 6086–6087. DOI:10.1128/JB.05953-11. PMC3194904. PMID21994921. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3194904.
  31. ^ Baliga, N. S.; Bonneau, R; Facciotti, MT; Pan, M; Glusman, G; Deutsch, EW; Shannon, P; Chiu, Y et al. (2004). "Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea". Genome Research 14 (11): 2221–34. DOI:10.1101/gr.2700304. PMC525680. PMID15520287. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=525680.
  32. ^ Pfeiffer F, Schuster SC, Broicher A, et al. (April 2008). "Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1". Genomics 91 (4): 335–346. DOI:10.1016/j.ygeno.2008.01.001. PMID18313895.
  33. ^ Ng, W. V.; Kennedy, SP; Mahairas, GG; Berquist, B; Pan, M; Shukla, HD; Lasky, SR; Baliga, NS et al. (2000). "Genome sequence of Halobacterium species NRC-1". Proceedings of the National Academy of Sciences 97 (22): 12176–81. DOI:10.1073/pnas.190337797. PMC17314. PMID11016950. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=17314.
  34. ^ Jiang X, Wang S, Cheng H, et al. (December 2011). "Genome sequence of Halobiforma lacisalsi AJ5, an extremely halophilic archaeon which harbors a bop gene". J. Bacteriol. 193 (24): 7023–7024. DOI:10.1128/JB.06282-11. PMC3232858. PMID22123770. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3232858.
  35. ^ Hartman, Amber L.; Norais, CéDric; Badger, Jonathan H.; Delmas, StéPhane; Haldenby, Sam; Madupu, Ramana; Robinson, Jeffrey; Khouri, Hoda et al. (2010). Friedberg, Iddo. ed. "The complete genome sequence of Haloferax volcanii DS2, a Model Archaeon". PLoS ONE 5 (3): e9605. DOI:10.1371/journal.pone.0009605. PMC2841640. PMID20333302. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2841640.
  36. ^ Malfatti S, Tindall BJ, Schneider S, et al. (September 24, 2009). "Complete genome sequence of Halogeometricum borinquense type strain (PR3)". Stand Genomic Sci. 1 (2): 150–159. DOI:10.4056/sigs.23264. PMC3035229. PMID21304651. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035229.
  37. ^ Tindall BJ, Schneider S, Lapidus A, et al. (November 22, 2009). "Complete genome sequence of Halomicrobium mukohataei type strain (arg-2)". Stand Genomic Sci. 1 (3): 270–277. DOI:10.4056/sigs.42644. PMC3035239. PMID21304667. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035239.
  38. ^ Dyall-Smith ML, Pfeiffer F, Klee K, et al. (2011). "Haloquadratum walsbyi: limited diversity in a global pond". PLoS ONE 6 (6): e20968. DOI:10.1371/journal.pone.0020968. PMC3119063. PMID21701686. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3119063.
  39. ^ Bolhuis H, Palm P, Wende A, et al. (July 4, 2006). "The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity". BMC Genomics 7: 169. DOI:10.1186/1471-2164-7-169. PMID16820047.
  40. ^ Antunes A, Alam I, Bajic VB, Stingl U (September 2011). "Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake". J. Bacteriol. 193 (17): 4553–4554. DOI:10.1128/JB.05462-11. PMC3165509. PMID21705593. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3165509.
  41. ^ "Complete genome sequence of Halorhabdus utahensis type strain (AX-2)". Stand Genomic Sci. 1 (3): 218–225. November 22, 2009. DOI:10.4056/sigs.31864. PMC3035240. PMID21304660. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035240.
  42. ^ Saunders, E.; Tindall, B. J.; Fähnrich, R.; Lapidus, A.; Copeland, A.; Del Rio, T. G.; Lucas, S.; Chen, F. et al. (2010). "Complete genome sequence of Haloterrigena turkmenica type strain (4kT)". Standards in Genomic Sciences 2 (1): 107–116. DOI:10.4056/sigs.681272. PMC3035258. PMID21304683. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035258. edit
  43. ^ Goo AH, Roach J, Glusman G, et al. (January 12, 2004). "Low-pass sequencing for microbial comparative genomics". BMC Genomics 5: 3. DOI:10.1186/1471-2164-5-3. PMID14718067.
  44. ^ Falb, M.; Pfeiffer, F; Palm, P; Rodewald, K; Hickmann, V; Tittor, J; Oesterhelt, D (2005). "Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis". Genome Research 15 (10): 1336–43. DOI:10.1101/gr.3952905. PMC1240075. PMID16169924. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1240075.
  45. ^ Smith, DR; D; D; L; D; A; B; B et al. (1997). "Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics". The Journal of Bacteriology 179 (22): 7135–55. PMC179657. PMID9371463. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=9371463.
  46. ^ Leahy SC, Kelly WJ, Altermann E, et al. (January 28, 2010). "The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions". PLoS ONE 5 (1): e8926. DOI:10.1371/journal.pone.0008926. PMC2812497. PMID20126622. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2812497.
  47. ^ Samuel BS, Hansen EE, Manchester JK, et al. (June 19, 2007). "Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut". PNAS 104 (25): 10643–8. DOI:10.1073/pnas.0704189104. PMC1890564. PMID17563350. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1890564.
  48. ^ a b c d e f g h i j k l m n o p q r s t Hansen EE, Lozupone CA, Rey FE, et al. (March 15, 2011). "Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins". PNAS 108 (Suppl 1): 4599–4606. DOI:10.1073/pnas.1000071108. PMC3063581. PMID21317366. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3063581.
  49. ^ Fricke, W. F.; Seedorf, H.; Henne, A.; Kruer, M.; Liesegang, H.; Hedderich, R.; Gottschalk, G.; Thauer, R. K. (2005). "The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis". J. Bacteriol. 188 (2): 642–58. DOI:10.1128/JB.188.2.642-658.2006. PMC1347301. PMID16385054. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347301.
  50. ^ Liesegang, H.; Kaster, A. -K.; Wiezer, A.; Goenrich, M.; Wollherr, A.; Seedorf, H.; Gottschalk, G.; Thauer, R. K. (2010). "Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism". Journal of Bacteriology 192 (21): 5850–5851. DOI:10.1128/JB.00844-10. PMC2953689. PMID20802048. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2953689. edit
  51. ^ Anderson I, Djao OD, Misra M, et al. (November 20, 2010). "Complete genome sequence of Methanothermus fervidus type strain (V24S)". Stand Genomic Sci. 3 (3): 315–324. DOI:10.4056/sigs.1283367. PMC3035299. PMID21304736. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035299.
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  53. ^ Hendrickson EL, Kaul R, Zhou Y, et al. (October 2004). "Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis". J Bacteriol. 186 (20): 6956–6969. DOI:10.1128/JB.186.20.6956-6969.2004. PMC522202. PMID15466049. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=522202.
  54. ^ Wang X, Greenfield P, Li D, et al. (October 2011). "Complete genome sequence of a nonculturable Methanococcus maripaludis strain extracted in a metagenomic survey of petroleum reservoir fluids". J Bacteriol. 193 (19): 6956–6969. DOI:10.1128/JB.05835-11. PMID21914896.
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  59. ^ Lu, Z.; Lu, Y. (2012). "Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil". Journal of Bacteriology 194 (9): 2398–2399. DOI:10.1128/JB.00207-12. PMC3347084. PMID22493204. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3347084. edit
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  61. ^ Anderson IJ, Sieprawska-Lupa M, Goltsman E, et al. (September 24, 2009). "Complete genome sequence of Methanocorpusculum labreanum type strain Z". Stand Genomic Sci. 1 (2): 197–203. DOI:10.4056/sigs.35575. PMC3035222. PMID21304657. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035222.
  62. ^ Anderson IJ, Sieprawska-Lupa M, Lapidus A, et al. (September 25, 2009). "Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1". Stand Genomic Sci. 1 (2): 189–196. DOI:10.4056/sigs.32535. PMC3035220. PMID21304656. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035220.
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  64. ^ Spring S, Scheuner C, Lapidus A, et al. (December 23, 2010). "The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments". Archaea 2010: 690737. DOI:10.1155/2010/690737. PMC3017947. PMID21234345. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3017947.
  65. ^ Brambilla E, Djao OD, Daligault H, et al. (October 27, 2010). "Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847)". Stand Genomic Sci. 3 (2): 203–211. DOI:10.4056/sigs.1183143. PMC3035365. PMID21304750. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3035365.
  66. ^ Galagan, J. E.; Nusbaum, C; Roy, A; Endrizzi, MG; MacDonald, P; Fitzhugh, W; Calvo, S; Engels, R et al. (2002). "The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity". Genome Research 12 (4): 532–42. DOI:10.1101/gr.223902. PMC187521. PMID11932238. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=187521.
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