1887

Abstract

During attempts to obtain novel, human-associated species of the domain , a coccoid micro-organism, designated strain B10, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and A gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10 produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO, strain B10 could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10 grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10 and several uncultured, methanogenic that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘ Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10 (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10 belongs to a novel order that is distinct from the . The novel strain also appeared to be distinct from DSM 3091 (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10 represents a novel species of a new genus for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is B10 ( = DSM 24529 = CSUR P135).

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2012-08-01
2019-10-23
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References

  1. Balch W. E., Fox G. E., Magrum L. J., Woese C. R., Wolfe R. S.. ( 1979;). Methanogens: reevaluation of a unique biological group. . Microbiol Rev 43:, 260–296.[PubMed]
    [Google Scholar]
  2. Belay N., Sparling R., Daniels L.. ( 1986;). Relationship of formate to growth and methanogenesis by Methanococcus thermolithotrophicus. . Appl Environ Microbiol 52:, 1080–1085.[PubMed]
    [Google Scholar]
  3. Boone D. R., Whitman W. B.. ( 1988;). Proposal of minimal standards for describing new taxa of methanogenic bacteria. . Int J Syst Bacteriol 38:, 212–219. [CrossRef]
    [Google Scholar]
  4. Cord-Ruwisch R., Ollivier B., Garcia J. L.. ( 1986;). Fructose degradation by Desulfovibrio sp. in pure culture and in coculture with Methanospirillum hungatei. . Curr Microbiol 13:, 285–289. [CrossRef]
    [Google Scholar]
  5. Dridi B., Henry M., El Khéchine A., Raoult D., Drancourt M.. ( 2009;). High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. . PLoS ONE 4:, e7063. [CrossRef][PubMed]
    [Google Scholar]
  6. Evans P. N., Hinds L. A., Sly L. I., McSweeney C. S., Morrison M., Wright A. D.. ( 2009;). Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii). . Appl Environ Microbiol 75:, 2598–2602. [CrossRef][PubMed]
    [Google Scholar]
  7. Ferrari A., Brusa T., Rutili A., Canzi E., Biavati B.. ( 1994;). Isolation and characterization of Methanobrevibacter oralis sp. nov.. Curr Microbiol 29:, 7–12. [CrossRef]
    [Google Scholar]
  8. Hallam S. J., Girguis P. R., Preston C. M., Richardson P. M., DeLong E. F.. ( 2003;). Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. . Appl Environ Microbiol 69:, 5483–5491. [CrossRef][PubMed]
    [Google Scholar]
  9. Hungate R. E., Macy J.. ( 1973;). The roll-tube method for cultivation of strict anaerobes. . Bull Ecol Res Comm 17:, 123–125.
    [Google Scholar]
  10. Jones J. B., Stadtman T. C.. ( 1977;). Methanococcus vannielii: culture and effects of selenium and tungsten on growth. . J Bacteriol 130:, 1404–1406.[PubMed]
    [Google Scholar]
  11. Jones J. B., Stadtman T. C.. ( 1981;). Selenium-dependent and selenium-independent formate dehydrogenases of Methanococcus vannielii. Separation of the two forms and characterization of the purified selenium-independent form. . J Biol Chem 256:, 656–663.[PubMed]
    [Google Scholar]
  12. Kendall M., Boone D.. ( 2006;). The order Methanosarcinales. . In The Prokaryotes: a Handbook on the Biology of Bacteria, , 3rd edn., vol. 3, pp. 244–256. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E... New York:: Springer;.
    [Google Scholar]
  13. Kumar S., Nei M., Dudley J., Tamura K.. ( 2008;). mega: a biologist-centric software for evolutionary analysis of DNA and protein sequences. . Brief Bioinform 9:, 299–306. [CrossRef][PubMed]
    [Google Scholar]
  14. Luton P. E., Wayne J. M., Sharp R. J., Riley P. W.. ( 2002;). The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. . Microbiology 148:, 3521–3530.[PubMed]
    [Google Scholar]
  15. Margulies M., Egholm M., Altman W. E., Attiya S., Bader J. S., Bemben L. A., Berka J., Braverman M. S., Chen Y. J.. & other authors ( 2005;). Genome sequencing in microfabricated high-density picolitre reactors. . Nature 437:, 376–380.[PubMed]
    [Google Scholar]
  16. Merhej V., Adékambi T., Pagnier I., Raoult D., Drancourt M.. ( 2008;). Yersinia massiliensis sp. nov., isolated from fresh water. . Int J Syst Evol Microbiol 58:, 779–784. [CrossRef][PubMed]
    [Google Scholar]
  17. Mihajlovski A., Alric M., Brugère J. F.. ( 2008;). A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. . Res Microbiol 159:, 516–521. [CrossRef][PubMed]
    [Google Scholar]
  18. Mihajlovski A., Dore J., Levenez F., Alric M., Brugere J. F.. ( 2010;). Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. . Environ Microbiol Rep 2:, 272–280. [CrossRef]
    [Google Scholar]
  19. Miller T. L., Wolin M. J.. ( 1985;). Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. . Arch Microbiol 141:, 116–122. [CrossRef][PubMed]
    [Google Scholar]
  20. Miller T. L., Wolin M. J., Conway de Macario E., Macario A. J.. ( 1982;). Isolation of Methanobrevibacter smithii from human feces. . Appl Environ Microbiol 43:, 227–232.[PubMed]
    [Google Scholar]
  21. Nehmé B., Gilbert Y., Létourneau V., Forster R. J., Veillette M., Villemur R., Duchaine C.. ( 2009;). Culture-independent characterization of archaeal biodiversity in swine confinement building bioaerosols. . Appl Environ Microbiol 75:, 5445–5450. [CrossRef][PubMed]
    [Google Scholar]
  22. Oxley A. P., Lanfranconi M. P., Würdemann D., Ott S., Schreiber S., McGenity T. J., Timmis K. N., Nogales B.. ( 2010;). Halophilic archaea in the human intestinal mucosa. . Environ Microbiol 12:, 2398–2410. [CrossRef][PubMed]
    [Google Scholar]
  23. Reysenbach A. L., Liu Y., Banta A. B., Beveridge T. J., Kirshtein J. D., Schouten S., Tivey M. K., Von Damm K. L., Voytek M. A.. ( 2006;). A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. . Nature 442:, 444–447. [CrossRef][PubMed]
    [Google Scholar]
  24. Rieu-Lesme F., Delbès C., Sollelis L.. ( 2005;). Recovery of partial 16S rDNA sequences suggests the presence of Crenarchaeota in the human digestive ecosystem. . Curr Microbiol 51:, 317–321. [CrossRef][PubMed]
    [Google Scholar]
  25. Saengkerdsub S., Anderson R. C., Wilkinson H. H., Kim W. K., Nisbet D. J., Ricke S. C.. ( 2007;). Identification and quantification of methanogenic Archaea in adult chicken ceca. . Appl Environ Microbiol 73:, 353–356. [CrossRef][PubMed]
    [Google Scholar]
  26. Samuel B. S., Hansen E. E., Manchester J. K., Coutinho P. M., Henrissat B., Fulton R., Latreille P., Kim K., Wilson R. K., Gordon J. I.. ( 2007;). Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. . Proc Natl Acad Sci U S A 104:, 10643–10648. [CrossRef][PubMed]
    [Google Scholar]
  27. Scanlan P. D., Shanahan F., Marchesi J. R.. ( 2008;). Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. . BMC Microbiol 8:, 79. [CrossRef][PubMed]
    [Google Scholar]
  28. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J.. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173:, 697–703.[PubMed]
    [Google Scholar]
  29. Wright A. D., Pimm C.. ( 2003;). Improved strategy for presumptive identification of methanogens using 16S riboprinting. . J Microbiol Methods 55:, 337–349. [CrossRef][PubMed]
    [Google Scholar]
  30. Wright A. D., Toovey A. F., Pimm C. L.. ( 2006;). Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveals more uncultured novel archaea. . Anaerobe 12:, 134–139. [CrossRef][PubMed]
    [Google Scholar]
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