1887

Abstract

Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5 was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5 was closely related to DSM 23967 (96.4 %) and to subsp. ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to DSM 20213 ( 94.1 %), DSM 23967 ( 91 %), DSM 100685 ( 80.3 %), subsp. ATCC 15697 ( 85.3 %) and subsp. ATCC 15708 ( 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising -Orn (Lys) – -Ser – -Ala – -Thr – -Ala. The DNA G+C content of strain TRI 5 was 60.9 mol%. Based on the data provided, strain TRI 5 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is TRI 5 (=DSM 103152=JCM 31790).

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2018-01-01
2024-03-29
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References

  1. Tannock GW. Normal Microflora – An Introduction to Microbes Inhabiting the Human Body London: Chapman & Hall; 1995
    [Google Scholar]
  2. Simpson JM, Martineau B, Jones WE, Ballam JM, Mackie RI. Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber. Microb Ecol 2002; 44:186–197 [View Article][PubMed]
    [Google Scholar]
  3. Endo A, Futagawa-Endo Y, Dicks LM. Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores. Anaerobe 2010; 16:590–596 [View Article][PubMed]
    [Google Scholar]
  4. Walter J. Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol 2008; 74:4985–4996 [View Article][PubMed]
    [Google Scholar]
  5. Xu B, Xu W, Yang F, Li J, Yang Y et al. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds. PLoS One 2013; 8:e56565 [View Article][PubMed]
    [Google Scholar]
  6. Garrity G, Bell J, Tg L. Taxonomic outline of the prokaryotes. In: Bergey’s Manual of Systematic Bacteriology New York; Berlin, Heidelberg: Springer; 2004
    [Google Scholar]
  7. Mattarelli P, Biavati B, Holzapfel WH, Wood BJ. The Bifidobacteria and Related Organisms: Biology, Taxonomy, Applications, 1st ed. Elsevier Science Publishing Co Inc; 2017
    [Google Scholar]
  8. Pechar R, Killer J, Švejstil R, Salmonová H, Geigerová M et al. Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica). Int J Syst Evol Microbiol 2017; 67:2403–2411 [View Article][PubMed]
    [Google Scholar]
  9. Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R et al. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 67: doi:10.1099/ijsem.0.002243 [View Article][PubMed]
    [Google Scholar]
  10. Mrázek J, Strosová L, Fliegerová K, Kott T, Kopecný J. Diversity of insect intestinal microflora. Folia Microbiol 2008; 53:229–233 [View Article][PubMed]
    [Google Scholar]
  11. Killer J, Kopečný J, Mrázek J, Koppová I, Havlík J et al. Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract. Int J Syst Evol Microbiol 2011; 61:1315–1321 [View Article][PubMed]
    [Google Scholar]
  12. Snowdon CT, Soini P. The tamarins, genus Saguinus . In Mittermeier RA, Rylands AB, Coimbra-Filho AF, Fonseca GAB. (editors) Ecology and Behavior of Neotropical Primates Washington, DC: WorldWidlife Fund; 1988 pp. 223–298
    [Google Scholar]
  13. Pinna C, Nannoni E, Rigoni G, Grandi M, Vecchiato CG et al. Effects of yogurt dietary supplementation on the intestinal ecosystem of a population of Emperor tamarins (Saguinus imperator). Prog Nutr 2015; 17:231–237
    [Google Scholar]
  14. Scardovi V. Genus Bifidobacterium . In Sneath PHA, Nair NS, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology Baltimore: The Williams & Wilkins Co; 1986 pp. 1418–1434
    [Google Scholar]
  15. Rada V, Sirotek K, Petr J. Evaluation of selective media for bifidobacteria in poultry and rabbit caecal samples. Zentralbl Veterinarmed B 1999; 46:369–373[PubMed]
    [Google Scholar]
  16. Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C et al. Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.). Syst Appl Microbiol 2016; 39:229–236 [View Article][PubMed]
    [Google Scholar]
  17. Masco L, Huys G, Gevers D, Verbrugghen L, Swings J. Identification of Bifidobacterium species using rep-PCR fingerprinting. Syst Appl Microbiol 2003; 26:557–563 [View Article][PubMed]
    [Google Scholar]
  18. Michelini S, Modesto M, Pisi A, Filippini G, Sandri C et al. Bifidobacterium eulemuris sp. nov. isolated from the faeces of the black lemur (Eulemur macaco). Int J Syst Evol Microbiol 2016; 66:1567–1576 [Crossref]
    [Google Scholar]
  19. Kim BJ, Kim HY, Yun YJ, Kim BJ, Kook YH. Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences. Int J Syst Evol Microbiol 2010; 60:2697–2704 [View Article][PubMed]
    [Google Scholar]
  20. Ventura M, Canchaya C, del Casale A, Dellaglio F, Neviani E et al. Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol 2006; 56:2783–2792 [View Article][PubMed]
    [Google Scholar]
  21. Cavalli-Sforza LL, Edwards AW. Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet 1967; 19:233–257[PubMed]
    [Google Scholar]
  22. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526[PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  25. Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F et al. Genomic encyclopedia of type strains of the genus Bifidobacterium . Appl Environ Microbiol 2014; 80:6290–6302 [View Article][PubMed]
    [Google Scholar]
  26. Martens M, Dawyndt P, Coopman R, Gillis M, de Vos P et al. 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 2008; 58:200–214 [View Article][PubMed]
    [Google Scholar]
  27. Jian W, Zhu L, Dong X. New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 2001; 51:1633–1638 [View Article][PubMed]
    [Google Scholar]
  28. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  29. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article][PubMed]
    [Google Scholar]
  30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  31. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120[PubMed] [Crossref]
    [Google Scholar]
  32. Cashion P, Holder-Franklin MA, McCully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
    [Google Scholar]
  33. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [Crossref]
    [Google Scholar]
  34. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [Crossref]
    [Google Scholar]
  35. Biavati B, Mattarelli P. Genus Bifidobacterium . In Goodfellow M, Kampfer P, Busse H-J, Suzuki K-I, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2012 pp. 171–206
    [Google Scholar]
  36. Killer J, Kopečný J, Mrázek J, Havlík J, Koppová I et al. Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol 2010; 33:359–366 [View Article][PubMed]
    [Google Scholar]
  37. Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C et al. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 2015; 65:1726–1734 [View Article][PubMed]
    [Google Scholar]
  38. Watanabe K, Makino H, Sasamoto M, Kudo Y, Fujimoto J et al. Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia. Int J Syst Evol Microbiol 2009; 59:1535–1540 [View Article][PubMed]
    [Google Scholar]
  39. Orban JI, Patterson JA. Modification of the phosphoketolase assay for rapid identification of bifidobacteria. J Microbiol Methods 2000; 40:221–224[PubMed] [Crossref]
    [Google Scholar]
  40. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129 [Crossref]
    [Google Scholar]
  41. Yanokura E, Oki K, Makino H, Modesto M, Pot B et al. Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets. Syst Appl Microbiol 2015; 38:305–314 [View Article][PubMed]
    [Google Scholar]
  42. Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LM. 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 2012; 35:92–97 [View Article][PubMed]
    [Google Scholar]
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