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Volume 66, Issue 3

sp. nov., isolated from faeces of black lemurs () Free

Abstract

Forty-three strains of bifidobacteria were isolated from the faeces of two adult black lemurs, . Thirty-four were identified as , recently described in . The nine remaining isolates were Gram-positive-staining, non-spore-forming, fructose-6-phosphate phosphoketolase-positive, microaerophilic, irregular rod-shaped bacteria that often presented Y- or V-shaped cells. Typing techniques revealed that these isolates were nearly identical, and strain LMM_E3 was chosen as a representative and characterized further. Phylogenetic analysis based on 16S rRNA gene sequences clustered this isolate inside the genus and showed the highest levels of sequence similarity with DSM 28807 (99.3 %), with LMG 21816 and subsp. ATCC 15697 (96.4 and 96.3 %, respectively) as the next most similar strains. The gene sequence of strain LMM_E3 showed the highest similarity to that of DSM 23968 (93.3 %), and 91.0 % similarity to that of the type strain of . DNA–DNA reassociation with the closest neighbour DSM 28807 was found to be 65.4 %. The DNA G+C content was 62.3 mol%. Strain LMM_E3 showed a peptidoglycan structure that has not been detected in bifidobacteria so far: A3α -Lys–-Ser–-Thr–-Ala. Based on the phylogenetic, genotypic and phenotypic data, strain LMM_E3 represents a novel species within the genus , for which the name sp. nov. is proposed; the type strain is LMM_E3 ( = DSM 100216 = JCM 30801).

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2016-03-01
2024-04-23
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References

  1. Baffoni L., Stenico V., Strahsburger E., Gaggìa F., Di Gioia D., Modesto M., Mattarelli P., Biavati B. 2013; Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment. BMC Microbiol 13:149 [View Article][PubMed]
     [Google Scholar]
  2. Biavati B., Mattarelli P. 2012; Genus Bifidobacterium . In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol. 5 pp 171–206Edited by Whitman W., Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M., Ludwig W., Suzuki K., Parte A. New York: Springer;
     [Google Scholar]
  3. Campanella J. J., Bitincka L., Smalley J. 2003; MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4:29–32 [View Article][PubMed]
     [Google Scholar]
  4. 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 [View Article][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. D'Aimmo M. R., Mattarelli P., Biavati B., Carlsson N. G., Andlid T. 2012; The potential of bifidobacteria as a source of natural folate. J Appl Microbiol 112:975–984 [View Article][PubMed]
     [Google Scholar]
  7. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142[PubMed] [CrossRef]
     [Google Scholar]
  8. Duranti S., Turroni F., Lugli G. A., Milani C., Viappiani A., Mangifesta M., Gioiosa L., Palanza P., van Sinderen D., Ventura M. 2014; Genomic characterization and transcriptional studies of the starch-utilizing strain Bifidobacterium adolescentis 22L. Appl Environ Microbiol 80:6080–6090 [View Article][PubMed]
     [Google Scholar]
  9. 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 [View Article][PubMed]
     [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
     [Google Scholar]
  11. 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]
  12. Huss V. A., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192[PubMed] [CrossRef]
     [Google Scholar]
  13. 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 [View Article][PubMed]
     [Google Scholar]
  14. Jolly A., Sussman R. W., Koyama N., Rasamimanana H. editors 2006 Ringtailed Lemur Biology: Lemur catta in Madagascar New York: Springer; [View Article]
     [Google Scholar]
  15. Junge R. E., Williams C. V., Campbell J. 2009; Nutrition and behavior of lemurs. Vet Clin North Am Exot Anim Pract 12:339–348 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  17. Killer J., Kopecný 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 [View Article][PubMed]
     [Google Scholar]
  18. Killer J., Kopečný J., Mrázek J., Havlík J., Koppová I., Benada O., Rada V., Kofronˇová O. 2010; Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol 33:359–366 [View Article][PubMed]
     [Google Scholar]
  19. Killer J., Kopečný J., Mrázek J., Koppová I., Havlík J., Benada O., Kott T. 2011; Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. Int J Syst Evol Microbiol 61:1315–1321 [View Article][PubMed]
     [Google Scholar]
  20. 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 [View Article][PubMed]
     [Google Scholar]
  21. Kim M., Oh H.-S., Park S.-C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  24. Masco L., Huys G., Gevers D., Verbrugghen L., Swings J. 2003; Identification of Bifidobacterium species using rep-PCR fingerprinting. Syst Appl Microbiol 26:557–563 [View Article][PubMed]
     [Google Scholar]
  25. Mattarelli P., Biavati B. 2014; The genera Bifidobacterium, Parascardovia and Scardovia . In Lactic Acid Bacteria: Biodiversity and Taxonomy pp 509–536Edited by Holzapfel W., Wood B. Chichester: Wiley; [View Article]
     [Google Scholar]
  26. Mattarelli P., Holzapfel W., Franz C.M.A.P., Endo A., Felis G. E., Hammes W., Pot B., Dicks L., Dellaglio F. 2014; Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 64:1434–1451 [View Article][PubMed]
     [Google Scholar]
  27. 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 39:159–167 [View Article]
     [Google Scholar]
  28. Michelini S., Modesto M., Oki K., Stenico V., Stefanini I., Biavati B., Watanabe K., Ferrara A., Mattarelli P. 2015; Isolation and identification of cultivable Bifidobacterium spp. from the faeces of 5 baby common marmosets (Callithrix jacchus L.). Anaerobe 33:101–104 [View Article][PubMed]
     [Google Scholar]
  29. Michelini S., Oki K., Yanokura E., Shimakawa Y., Modesto M., Mattarelli P., Biavati B., Watanabe K. 2016; Bifidobacterium myosotis sp. nov., Bifidobacterium tissierisp. nov. and Bifidobacterium hapali sp. nov. three novel taxa from the faeces of baby common marmosets (Callithrix jacchusL.). Int J Syst Evol Microbiol (in press) [View Article][PubMed]
     [Google Scholar]
  30. Modesto M., Michelini S., Stefanini I., Ferrara A., Tacconi S., Biavati B., Mattarelli P. 2014; Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 64:2819–2827 [View Article][PubMed]
     [Google Scholar]
  31. Modesto M., Michelini S., Stefanini I., Sandri C., Spiezio C., Pisi A., Filippini G., Biavati B., Mattarelli P. 2015; Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 65:1726–1734 [View Article][PubMed]
     [Google Scholar]
  32. Myers E. W., Miller W. 1988; Optimal alignments in linear space. Comput Appl Biosci 4:11–17[PubMed]
     [Google Scholar]
  33. Orban J. I., Patterson J. A. 2000; Modification of the phosphoketolase assay for rapid identification of bifidobacteria. J Microbiol Methods 40:221–224 [View Article][PubMed]
     [Google Scholar]
  34. Pineiro M., Stanton C. 2007; Probiotic bacteria: legislative framework – requirements to evidence basis. J Nutr 137:(Suppl. 2)850S–853S[PubMed]
     [Google Scholar]
  35. 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 [View Article][PubMed]
     [Google Scholar]
  36. Sauther M. L., Sussman R. W., Gould L. 1999; The socioecology of the ringtailed lemur: thirty-five years of research. Evol Anthropol 8:120–132 [View Article]
     [Google Scholar]
  37. Scardovi V. 1986; Genus Bifidobacterium . In Bergey's Manual of Systematic Bacteriology vol. 2 pp 1418–1434Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
     [Google Scholar]
  38. Schumann P. 2011; Peptidoglycan structure. Methods Microbiol 38:101–129 [View Article]
     [Google Scholar]
  39. Talavera G., Castresana J. 2007; Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577 [View Article][PubMed]
     [Google Scholar]
  40. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
     [Google Scholar]
  41. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  42. Tsuchida S., Takahashi S., Nguema P. P., Fujita S., Kitahara M., Yamagiwa J., Ngomanda A., Ohkuma M., Ushida K. 2014; Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 64:449–455 [View Article][PubMed]
     [Google Scholar]
  43. Turroni F., van Sinderen D., Ventura M. 2011; Genomics and ecological overview of the genus Bifidobacterium . Int J Food Microbiol 149:37–44 [View Article][PubMed]
     [Google Scholar]
  44. Ushida K., Uwatoko Y., Adachi Y., Soumah A. G., Matsuzawa T. 2010; Isolation of bifidobacteria from feces of chimpanzees in the wild. J Gen Appl Microbiol 56:57–60 [View Article][PubMed]
     [Google Scholar]
  45. 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 [View Article][PubMed]
     [Google Scholar]
  46. 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 [View Article][PubMed]
     [Google Scholar]
  47. 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 [View Article][PubMed]
     [Google Scholar]
  48. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
     [Google Scholar]
  49. Yildirim S., Yeoman C. J., Sipos M., Torralba M., Wilson B. A., Goldberg T. L., Stumpf R. M., Leigh S. R., White B. A., Nelson K. E. 2010; Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities. PLoS One 5:e13963 [View Article][PubMed]
     [Google Scholar]
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Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco)
Int J Syst Evol Microbiol 66, 1567 (2016); https://doi.org/10.1099/ijsem.0.000924
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