1887

Abstract

A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by . The results of the similarity search indicated that the bacterium belongs to the class , family . It showed maximum sequence similarity (96.5 %) with CCUG 39967 followed by DSM 17166 (96.1 %) and LMG 19572 (95.3 %). The DNA G+C content of strain HM-7 was 42 mol%. Strain HM-7 contained C, C, C 3-OH and C as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7 represents a member of the genus , but at the same time distinguished it from CCUG 39967, the only species of the genus with a validly published name. Based on polyphasic characterization we conclude that the bacterium represents a novel species of the genus and propose the name sp. nov., with strain HM-7 ( = MCC 2185 = DSM 27484) as the type strain of the species.

Funding
This study was supported by the:
  • Department of Biotechnology (DBT) Government of India (Award BT/PR/0054/NDB/52/94/2007)
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2014-04-01
2024-05-09
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References

  1. Blümel S., Mark B., Busse H.-J., Kämpfer P., Stolz A. ( 2001 ). Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. . Int J Syst Evol Microbiol 51, 18671871. [View Article] [PubMed]
    [Google Scholar]
  2. Coenye T., Vanlaere E., Samyn E., Falsen E., Larsson P., Vandamme P. ( 2005 ). Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples. . Int J Syst Evol Microbiol 55, 251256. [View Article] [PubMed]
    [Google Scholar]
  3. De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J. B., Massart S., Collini S., Pieraccini G., Lionetti P. ( 2010 ). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. . Proc Natl Acad Sci U S A 107, 1469114696. [View Article] [PubMed]
    [Google Scholar]
  4. De Ley J., Segers P., Kersters K., Mannheim W., Lievens A. ( 1986 ). Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family Alcaligenaceae . . Int J Syst Bacteriol 36, 405414. [View Article]
    [Google Scholar]
  5. Fujimura K. E., Slusher N. A., Cabana M. D., Lynch S. V. ( 2010 ). Role of the gut microbiota in defining human health. . Expert Rev Anti Infect Ther 8, 435454. [View Article] [PubMed]
    [Google Scholar]
  6. Ghosh W., Bagchi A., Mandal S., Dam B., Roy P. ( 2005 ). Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India. . Int J Syst Evol Microbiol 55, 17791787. [View Article] [PubMed]
    [Google Scholar]
  7. Gibello A., Vela A. I., Martín M., Barra-Caracciolo A., Grenni P., Fernández-Garayzábal J. F. ( 2009 ). Reclassification of the members of the genus Tetrathiobacter Ghosh et al. 2005 to the genus Advenella Coenye et al. 2005. . Int J Syst Evol Microbiol 59, 19141918. [View Article] [PubMed]
    [Google Scholar]
  8. Gill S. R., Pop M., Deboy R. T., Eckburg P. B., Turnbaugh P. J., Samuel B. S., Gordon J. I., Relman D. A., Fraser-Liggett C. M., Nelson K. E. ( 2006 ). Metagenomic analysis of the human distal gut microbiome. . Science 312, 13551359. [View Article] [PubMed]
    [Google Scholar]
  9. Gonzalez J. M., Saiz-Jimenez C. ( 2002 ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4, 770773. [View Article] [PubMed]
    [Google Scholar]
  10. Hakansson A., Molin G. ( 2011 ). Gut microbiota and inflammation. . Nutrients 3, 637682. [View Article] [PubMed]
    [Google Scholar]
  11. Jang S. S., Donahue J. M., Arata A. B., Goris J., Hansen L. M., Earley D. L., Vandamme P. A. R., Timoney P. J., Hirsh D. C. ( 2001 ). Taylorella asinigenitalis sp. nov., a bacterium isolated from the genital tract of male donkeys (Equus asinus). . Int J Syst Evol Microbiol 51, 971976. [View Article] [PubMed]
    [Google Scholar]
  12. Kallus S. J., Brandt L. J. ( 2012 ). The intestinal microbiota and obesity. . J Clin Gastroenterol 46, 1624. [View Article] [PubMed]
    [Google Scholar]
  13. Kau A. L., Ahern P. P., Griffin N. W., Goodman A. L., Gordon J. I. ( 2011 ). Human nutrition, the gut microbiome and the immune system. . Nature 474, 327336. [View Article] [PubMed]
    [Google Scholar]
  14. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  15. Marmur J. ( 1961 ). A procedure for isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  16. Prakash O., Kumari K., Lal R. ( 2007 ). Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. . Int J Syst Evol Microbiol 57, 527531. [View Article] [PubMed]
    [Google Scholar]
  17. Prakash O., Green S. J., Jasrotia P., Overholt W. A., Canion A., Watson D. B., Brooks S. C., Kostka J. E. ( 2012 ). Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. . Int J Syst Evol Microbiol 62, 24572462. [View Article] [PubMed]
    [Google Scholar]
  18. Prakash O., Nimonkar Y., Shouche Y. S. ( 2013a ). Practice and prospects of microbial preservation. . FEMS Microbiol Lett 339, 19. [View Article] [PubMed]
    [Google Scholar]
  19. Prakash O., Shouche Y., Jangid K., Kostka J. E. ( 2013b ). Microbial cultivation and the role of microbial resource centers in the omics era. . Appl Microbiol Biotechnol 97, 5162. [View Article] [PubMed]
    [Google Scholar]
  20. Qin J., Li R., Raes J., Arumugam M., Burgdorf K. S., Manichanh C., Nielsen T., Pons N., Levenez F. & other authors ( 2010 ). A human gut microbial gene catalogue established by metagenomic sequencing. . Nature 464, 5965. [View Article] [PubMed]
    [Google Scholar]
  21. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical note 101. Newark, DE:: MIDI Inc;.
    [Google Scholar]
  22. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E. , Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  23. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152155.
    [Google Scholar]
  24. Stackebrandt E., Goebel B. M. ( 1994 ). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44, 846849. [View Article]
    [Google Scholar]
  25. Sweeney T. E., Morton J. M. ( 2013 ). The human gut microbiome: a review of the effect of obesity and surgically induced weight loss. . JAMA Surg 148, 563569. [View Article] [PubMed]
    [Google Scholar]
  26. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  27. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. ( 1997 ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25, 48764882. [View Article] [PubMed]
    [Google Scholar]
  28. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [View Article] [PubMed]
    [Google Scholar]
  29. Tsai F., Coyle W. J. ( 2009 ). The microbiome and obesity: is obesity linked to our gut flora. ? Curr Gastroenterol Rep 11, 307313. [View Article] [PubMed]
    [Google Scholar]
  30. Vandamme P., Segers P., Ryll M., Hommez J., Vancanneyt M., Coopman R., De Baere R., Van de Peer Y., Kersters K. & other authors ( 1998 ). Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation. . Int J Syst Bacteriol 48, 431440. [View Article] [PubMed]
    [Google Scholar]
  31. Weckman B. G., Catlin B. W. ( 1957 ). Deoxyribonuclease activity of micrococci from clinical sources. . J Bacteriol 73, 747753.[PubMed]
    [Google Scholar]
  32. Wübbeler J. H., Lütke-Eversloh T., Van Trappen S., Vandamme P., Steinbüchel A. ( 2006 ). Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid. . Int J Syst Evol Microbiol 56, 13051310. [View Article] [PubMed]
    [Google Scholar]
  33. Zhang X., Shen D., Fang Z., Jie Z., Qiu X., Zhang C., Chen Y., Ji L. ( 2013 ). Human gut microbiota changes reveal the progression of glucose intolerance. . PLoS ONE 8, e71108. [View Article] [PubMed]
    [Google Scholar]
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