1887

Abstract

A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated bacterium ACC2 strain DSM 24645 was isolated from human subgingival dental plaque. Bacterial cells were 4–40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30–42 °C and 4.9–7.5, respectively. Major fatty acids were C, C DMA (dimethyl aldehyde), C, Cω7 DMA. The whole-cell hydrolysate contained -diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645 formed, together with several uncultured oral clones, a separate branch within the family , with the highest sequence similarity to the type strain of at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645 represents a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is DSM 24645 ( = HM-480; deposited in BEI Resources, an NIH collection managed by the ATCC).

Funding
This study was supported by the:
  • NIH (Award 3 R21 DE018026-02S1 and 1RC1DE020707-01)
  • NSF (Award EF-1002148 and EAR-0920718)
  • US Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division (Award DE-AC02-07CH11358)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.042812-0
2013-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/4/1450.html?itemId=/content/journal/ijsem/10.1099/ijs.0.042812-0&mimeType=html&fmt=ahah

References

  1. Aziz R. K., Bartels D., Best A. A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M. & other authors ( 2008 ). The RAST Server: rapid annotations using subsystems technology. . BMC Genomics 9, 75. [View Article] [PubMed]
    [Google Scholar]
  2. Brook I., Frazier E. H., Gher M. E. ( 1991 ). Aerobic and anaerobic microbiology of periapical abscess. . Oral Microbiol Immunol 6, 123125. [View Article] [PubMed]
    [Google Scholar]
  3. Carlier J. P., K’ouas G., Bonne I., Lozniewski A., Mory F. ( 2004 ). Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes). . Int J Syst Evol Microbiol 54, 16111615. [View Article] [PubMed]
    [Google Scholar]
  4. Carlier J. P., K’ouas G., Han X. Y. ( 2007 ). Moryella indoligenes gen. nov., sp. nov., an anaerobic bacterium isolated from clinical specimens. . Int J Syst Evol Microbiol 57, 725729. [View Article] [PubMed]
    [Google Scholar]
  5. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  6. Cotta M. A., Whitehead T. R., Falsen E., Moore E., Lawson P. A. ( 2009 ). Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source. . Int J Syst Evol Microbiol 59, 150155. [View Article] [PubMed]
    [Google Scholar]
  7. Daniluk T., Tokajuk G., Cylwik-Rokicka D., Rozkiewicz D., Zaremba M. L., Stokowska W. ( 2006 ). Aerobic and anaerobic bacteria in subgingival and supragingival plaques of adult patients with periodontal disease. . Adv Med Sci 51 (Suppl. 1), 8185.[PubMed]
    [Google Scholar]
  8. Dewhirst F. E., Chen T., Izard J., Paster B. J., Tanner A. C., Yu W. H., Lakshmanan A., Wade W. G. ( 2010 ). The human oral microbiome. . J Bacteriol 192, 50025017. [View Article] [PubMed]
    [Google Scholar]
  9. Downes J., Munson M. A., Radford D. R., Spratt D. A., Wade W. G. ( 2002 ). Shuttleworthia satelles gen. nov., sp. nov., isolated from the human oral cavity. . Int J Syst Evol Microbiol 52, 14691475. [View Article] [PubMed]
    [Google Scholar]
  10. Duncan S. H., Hold G. L., Barcenilla A., Stewart C. S., Flint H. J. ( 2002 ). Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. . Int J Syst Evol Microbiol 52, 16151620. [View Article] [PubMed]
    [Google Scholar]
  11. Ellis E. A. ( 2006 ). Solutions to the problem of substitution of ERL 4221 for vinyl cyclohexene dioxide in Spurr low viscosity embedding formulations. . Microsc Today 14, 3233.
    [Google Scholar]
  12. Frazzon J., Dean D. R. ( 2003 ). Formation of iron-sulfur clusters in bacteria: an emerging field in bioinorganic chemistry. . Curr Opin Chem Biol 7, 166173. [View Article] [PubMed]
    [Google Scholar]
  13. Jones H. E., Trudinger P. A., Chambers L. A., Pyliotis N. A. ( 1976 ). Metal accumulation by bacteria with particular reference to dissimilatory sulphate-reducing bacteria. . Z Allg Mikrobiol 16, 425435. [View Article] [PubMed]
    [Google Scholar]
  14. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C Content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  15. Mihara H., Esaki N. ( 2002 ). Bacterial cysteine desulfurases: their function and mechanisms. . Appl Microbiol Biotechnol 60, 1223. [View Article] [PubMed]
    [Google Scholar]
  16. Moore L. V., Moore W. E. ( 1994 ). Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., anaerobic gram-negative bacilli from the human gingival crevice. . Int J Syst Bacteriol 44, 187192. [View Article] [PubMed]
    [Google Scholar]
  17. Müller S. A., Engel A. ( 2006 ). Biological scanning transmission electron microscopy. imaging and single molecule mass determination. . CHIMIA Int J Chem 60, 749753. [CrossRef]
    [Google Scholar]
  18. Paster B. J., Boches S. K., Galvin J. L., Ericson R. E., Lau C. N., Levanos V. A., Sahasrabudhe A., Dewhirst F. E. ( 2001 ). Bacterial diversity in human subgingival plaque. . J Bacteriol 183, 37703783. [View Article] [PubMed]
    [Google Scholar]
  19. Pósfai M., Buseck P. R., Bazylinski D. A., Frankel R. B. ( 1998 ). Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers. . Science 280, 880883. [View Article] [PubMed]
    [Google Scholar]
  20. Rainey, F. A. (2009). Family V. Lachnospiraceae fam. nov. In Bergey’s Manual of Systematic Bacteriology, vol. 3, The Firmicutes, pp. 921–968. Edited by P. De Vos, G. M. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K.-H. Schleifer & W. B. Whitman. New York: Springer.
  21. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  22. Schumann P. ( 2011 ). Peptidoglycan Structure. . In Taxonomy of Prokaryotes, Methods in Microbiology, vol. 38, pp. 101129. Edited by Rainey F., Oren A. . London:: Academic Press;. [View Article]
    [Google Scholar]
  23. Sizova M. V., Hohmann T., Hazen A., Paster B. J., Halem S. R., Murphy C. M., Panikov N. S., Epstein S. S. ( 2012 ). New approaches for isolation of previously uncultivated oral bacteria. . Appl Environ Microbiol 78, 194203. [View Article] [PubMed]
    [Google Scholar]
  24. Sousa A. A., Hohmann-Marriott M., Aronova M. A., Zhang G., Leapman R. D. ( 2008 ). Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM. . J Struct Biol 162, 1428. [View Article] [PubMed]
    [Google Scholar]
  25. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  26. Taras D., Simmering R., Collins M. D., Lawson P. A., Blaut M. ( 2002 ). Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces. . Int J Syst Evol Microbiol 52, 423428.[PubMed]
    [Google Scholar]
  27. 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]
  28. Willems A., Collins M. D. ( 1995 ). Evidence for the placement of the gram-negative Catonella morbi (Moore and Moore) and Johnsonella ignava (Moore and Moore) within the Clostridium subphylum of the gram-positive bacteria on the basis of 16S rRNA sequences. . Int J Syst Bacteriol 45, 855857. [View Article] [PubMed]
    [Google Scholar]
  29. Yarza P., Richter M., Peplies J., Euzéby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. ( 2008 ). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. . Syst Appl Microbiol 31, 241250. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.042812-0
Loading
/content/journal/ijsem/10.1099/ijs.0.042812-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error