1887

Abstract

Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a ‘Y’ shape. Strains MRM 3/1 and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1 showed a peptidoglycan type unique among members of the genus . The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, , and gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1 and MRM 4/2 had the highest similarities to DSM 13734 (94.6 %) and DSM 23968 (94.5 %). Analysis of showed that both strains were closely related to DSM 23968 (97.5 % similarity); however, despite this high degree of similarity, our isolates could be distinguished from DSM 23968 by low levels of DNA–DNA relatedness (30.4 % with MRM 3/1). Strains MRM 3/1 and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus than to other genera in the family . On the basis of these results, strains MRM 3/1 and MRM 4/2 represent a novel species within the genus , for which the name sp. nov. is proposed; the type strain is MRM 3/1 ( = DSM 26737 = JCM 18761).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.056937-0
2014-08-01
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/8/2819.html?itemId=/content/journal/ijsem/10.1099/ijs.0.056937-0&mimeType=html&fmt=ahah

References

  1. Bailey M. T. , Coe C. L. . ( 2002; ). Intestinal microbial patterns of the common marmoset and rhesus macaque. . Comp Biochem Physiol A Mol Integr Physiol 133:, 379–388. [CrossRef] [PubMed]
    [Google Scholar]
  2. Biavati B. , Mattarelli P. . ( 2012; ). Genus Bifidobacterium . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp. 171–206. Edited by Goodfellow M. , Kämpfer P. , Busse H.-J. , Suzuki K. , Ludwig W. , Whitman W. B. . . New York:: Springer;.
    [Google Scholar]
  3. 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:, 461–466. [CrossRef] [PubMed]
    [Google Scholar]
  4. Caton J. M. , Hill D. M. , Hume I. D. , Crook G. A. . ( 1996; ). The digestive strategy of the common marmoset, Callithrix jacchus . . Comp Biochem Physiol A Physiol 114:, 1–8. [CrossRef] [PubMed]
    [Google Scholar]
  5. Cavalli-Sforza L. L. , Edwards A. W. F. . ( 1967; ). Phylogenetic analysis. Models and estimation procedures. . Am J Hum Genet 19:, 233–257.[PubMed]
    [Google Scholar]
  6. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  7. Endo A. , Futagawa-Endo Y. , Schumann P. , Pukall R. , Dicks L. M. T. . ( 2012; ). Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas). . Syst Appl Microbiol 35:, 92–97. [CrossRef] [PubMed]
    [Google Scholar]
  8. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Fitch W. M. . ( 1971; ). Toward defining the course of evolution: minimum change for a specified tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  10. Fitch W. M. , Margoliash E. . ( 1967; ). Construction of phylogenetic trees. . Science 155:, 279–284. [CrossRef] [PubMed]
    [Google Scholar]
  11. Hall T. A. . ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41:, 95–98.
    [Google Scholar]
  12. Holdeman L. V. , Cato E. P. , Moore W. E. C. . ( 1977; ). Anaerobic Laboratory Manual, , 4th edn.. Blacksburg, VA:: Virginia Polytechnic and State University;.
    [Google Scholar]
  13. Huang X. . ( 1992; ). A contig assembly program based on sensitive detection of fragment overlaps. . Genomics 14:, 18–25. [CrossRef] [PubMed]
    [Google Scholar]
  14. Huss V. A. R. , Festl H. , Schleifer K. H. . ( 1983; ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4:, 184–192. [CrossRef] [PubMed]
    [Google Scholar]
  15. Jian W. , Zhu L. , Dong X. . ( 2001; ). New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. . Int J Syst Evol Microbiol 51:, 1633–1638. [CrossRef] [PubMed]
    [Google Scholar]
  16. Katoh K. , Standley D. M. . ( 2013; ). mafft multiple sequence alignment software version 7: improvements in performance and usability. . Mol Biol Evol 30:, 772–780. [CrossRef] [PubMed]
    [Google Scholar]
  17. Killer J. , Kopečný J. , Mrázek J. , Rada V. , Benada O. , Koppová I. , Havlík J. , Straka J. . ( 2009; ). Bifidobacterium bombi sp. nov., from the bumblebee digestive tract. . Int J Syst Evol Microbiol 59:, 2020–2024. [CrossRef] [PubMed]
    [Google Scholar]
  18. Kim B. J. , Kim H. Y. , Yun Y. J. , Kim B. J. , Kook Y. H. . ( 2010; ). Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences. . Int J Syst Evol Microbiol 60:, 2697–2704. [CrossRef] [PubMed]
    [Google Scholar]
  19. Killer J. , Kopecny J. , Mrazek J. , Koppová I. , Havlík J. , Benada O. , Kott T. . ( 2010; ). Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. . Int J Syst Evol Microbiol 61:, 1315–1321. [CrossRef]
    [Google Scholar]
  20. 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:, 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  21. Kimura M. . ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  22. Kopečný J. , Mrázek J. , Killer J. . ( 2010; ). The presence of bifidobacteria in social insects, fish and reptiles. . Folia Microbiol (Praha) 55:, 336–339. [CrossRef] [PubMed]
    [Google Scholar]
  23. Martens M. , Dawyndt P. , Coopman R. , Gillis M. , De Vos P. , Willems A. . ( 2008; ). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). . Int J Syst Evol Microbiol 58:, 200–214. [CrossRef] [PubMed]
    [Google Scholar]
  24. Mesbah M. , Premachandran U. , Whitman W. . ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  25. Orban J. I. , Patterson J. A. . ( 2000; ). Modification of the phosphoketolase assay for rapid identification of bifidobacteria. . J Microbiol Methods 40:, 221–224. [CrossRef] [PubMed]
    [Google Scholar]
  26. Pineiro M. , Stanton C. . ( 2007; ). Probiotic bacteria: legislative framework – requirements to evidence basis. . J Nutr 137: (Suppl. 2), 850S–853S.[PubMed]
    [Google Scholar]
  27. Rada V. , Petr J. . ( 2000; ). A new selective medium for the isolation of glucose non-fermenting bifidobacteria from hen caeca. . J Microbiol Methods 43:, 127–132. [CrossRef] [PubMed]
    [Google Scholar]
  28. Rossi M. , Altomare L. , Gonzàlez Vara y Rodriguez A. , Brigidi P. , Matteuzzi D. . ( 2000; ). Nucleotide sequence, expression and transcriptional analysis of the Bifidobacterium longum MB 219 lacZ gene. . Arch Microbiol 174:, 74–80. [CrossRef] [PubMed]
    [Google Scholar]
  29. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  30. Scardovi V. . ( 1986; ). Genus Bifidobacterium Orla-Jensen. . In Bergey’s Manual of Systematic Bacteriology, vol. 2, pp. 1418–1434. Edited by Sneath P. H. A. , Mair N. S. , Sharpe M. E. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  31. Stenico V. , Michelini S. , Modesto M. , Baffoni L. , Mattarelli P. , Biavati B. . ( 2014; ). Identification of Bifidobacterium spp. using hsp60 PCR-RFLP analysis: an update. . Anaerobe 26:, 36–40. [CrossRef] [PubMed]
    [Google Scholar]
  32. Talavera G. , Castresana J. . ( 2007; ). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. . Syst Biol 56:, 564–577. [CrossRef] [PubMed]
    [Google Scholar]
  33. Tamaoka J. , Komagata K. . ( 1984; ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25:, 125–128. [CrossRef]
    [Google Scholar]
  34. 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:, 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  35. 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:, 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  36. 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:, 249–266. [CrossRef]
    [Google Scholar]
  37. Turroni F. , van Sinderen D. , Ventura M. . ( 2011; ). Genomics and ecological overview of the genus Bifidobacterium . . Int J Food Microbiol 149:, 37–44. [CrossRef] [PubMed]
    [Google Scholar]
  38. Ventura M. , Meylan V. , Zink R. . ( 2003; ). Identification and tracing of Bifidobacterium species by use of enterobacterial repetitive intergenic consensus sequences. . Appl Environ Microbiol 69:, 4296–4301. [CrossRef] [PubMed]
    [Google Scholar]
  39. Ventura M. , van Sinderen D. , Fitzgerald G. F. , Zink R. . ( 2004; ). Insights into the taxonomy, genetics and physiology of bifidobacteria. . Antonie van Leeuwenhoek 86:, 205–223. [CrossRef] [PubMed]
    [Google Scholar]
  40. Ventura M. , Canchaya C. , Del Casale A. , Dellaglio F. , Neviani E. , Fitzgerald G. F. , van Sinderen D. . ( 2006; ). Analysis of bifidobacterial evolution using a multilocus approach. . Int J Syst Evol Microbiol 56:, 2783–2792. [CrossRef] [PubMed]
    [Google Scholar]
  41. Watanabe K. , Makino H. , Sasamoto M. , Kudo Y. , Fujimoto J. , Demberel S. . ( 2009; ). Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare’s milk product from Mongolia. . Int J Syst Evol Microbiol 59:, 1535–1540. [CrossRef] [PubMed]
    [Google Scholar]
  42. Zhu L. , Li W. , Dong X. . ( 2003; ). Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov. . Int J Syst Evol Microbiol 53:, 1619–1623. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.056937-0
Loading
/content/journal/ijsem/10.1099/ijs.0.056937-0
Loading

Data & Media loading...

Supplements

Supplementary Material 

PDF

Most Cited This Month

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