1887

Abstract

Two strains, i.e., 2176B and 2177B, were isolated from Golden-Headed Lion Tamarin () and Goeldi's monkey (). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and -fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including 60, B, J, G and C genes) and the core genome revealed that bifidobacterial strains 2176B and 2177B exhibit close phylogenetic relatedness to DSM 103139 and LMG 11041, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized species. Thus, sp. nov. (2176B=LMG 31469=CCUG 73785) and sp. nov. (2177B=LMG 31471=CCUG 73786 are proposed as novel species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004032
2020-02-17
2020-06-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2288.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004032&mimeType=html&fmt=ahah

References

  1. Bergey DG, WB W, Parte AC. The actinobacteria. Bergey’s Manual of Systematic Bacteriology 2012
    [Google Scholar]
  2. 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 [CrossRef]
    [Google Scholar]
  3. Zhang G, Gao B, Adeolu M, Khadka B, Gupta RS. Phylogenomic analyses and comparative studies on genomes of the Bifidobacteriales: identification of molecular signatures specific for the order Bifidobacteriales and its different Subclades. Front Microbiol 2016; 7:978 [CrossRef]
    [Google Scholar]
  4. Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C et al. Corrigendum to "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. 39 (2016) 229-236]. Syst Appl Microbiol 2018
    [Google Scholar]
  5. Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C et al. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst Appl Microbiol 2018; 41:173–183 [CrossRef]
    [Google Scholar]
  6. Modesto M, Michelini S, Oki K, Biavati B, Watanabe K et al. Bifidobacterium catulorum sp. nov., a novel taxon from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2018; 68:575–581 [CrossRef]
    [Google Scholar]
  7. Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D et al. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2018; 68:141–148 [CrossRef]
    [Google Scholar]
  8. 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; 67:3987–3995 [CrossRef]
    [Google Scholar]
  9. Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R et al. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349–2356 [CrossRef]
    [Google Scholar]
  10. 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 [CrossRef]
    [Google Scholar]
  11. Michelini S, Modesto M, Pisi AM, Filippini G, Sandri C et al. Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco). Int J Syst Evol Microbiol 2016; 66:1567–1576 [CrossRef]
    [Google Scholar]
  12. Laureys D, Cnockaert M, De Vuyst L, Vandamme P. Bifidobacterium aquikefiri sp. nov., isolated from water kefir. Int J Syst Evol Microbiol 2016; 66:1281–1286 [CrossRef]
    [Google Scholar]
  13. Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M et al. Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.). Int J Syst Evol Microbiol 2016; 66:255–265 [CrossRef]
    [Google Scholar]
  14. Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C et al. Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Appl Environ Microbiol 2014; 80:6383–6394 [CrossRef]
    [Google Scholar]
  15. Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L et al. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 2017; 18:568 [CrossRef]
    [Google Scholar]
  16. Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C et al. Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. Int J Syst Evol Microbiol 2019; 69:1288–1298 [CrossRef]
    [Google Scholar]
  17. Ventura M, van Sinderen D, Fitzgerald GF, Zink R. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie van Leeuwenhoek 2004; 86:205–223 [CrossRef]
    [Google Scholar]
  18. Turroni F, van Sinderen D, Ventura M. Genomics and ecological overview of the genus Bifidobacterium . Int J Food Microbiol 2011; 149:37–44 [CrossRef]
    [Google Scholar]
  19. Ventura M, Turroni F, Lugli GA, van Sinderen D. Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. J Sci Food Agric 2014; 94:163–168 [CrossRef]
    [Google Scholar]
  20. Alberoni D, Gaggìa F, Baffoni L, Modesto MM, Biavati B et al. Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract. Syst Appl Microbiol 2019; 42:205–216 [CrossRef]
    [Google Scholar]
  21. Modesto M, Watanabe K, Arita M, Satti M, Oki K et al. Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2019; 69:2477–2485 [CrossRef]
    [Google Scholar]
  22. Milani C, Mangifesta M, Mancabelli L, Lugli GA, James K et al. Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life. Isme J 2017; 11:2834–2847 [CrossRef]
    [Google Scholar]
  23. Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F et al. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 2017; 5:66 [CrossRef]
    [Google Scholar]
  24. Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA et al. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103–118 [CrossRef]
    [Google Scholar]
  25. Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A et al. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl Environ Microbiol 2009; 75:1534–1545 [CrossRef]
    [Google Scholar]
  26. Ventura M, Zink R. Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis . Appl Environ Microbiol 2002; 68:6429–6434 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L et al. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep 2015; 5:15782 [CrossRef]
    [Google Scholar]
  29. Duranti S, Milani C, Lugli GA, Mancabelli L, Turroni F et al. Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis . Sci Rep 2016; 6:23971 [CrossRef]
    [Google Scholar]
  30. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation. FEMS Microbiol Lett 2016; 363:fnw049 [CrossRef]
    [Google Scholar]
  31. Duranti S, Milani C, Lugli GA, Turroni F, Mancabelli L et al. Insights from genomes of representatives of the human gut commensal B ifidobacterium bifidum . Environ Microbiol 2015; 17:2515–2531 [CrossRef]
    [Google Scholar]
  32. Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M et al. Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach. Appl Environ Microbiol 2018; 84:
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. Zhao J, Zhang S, Wu L-Y, Zhang X-S. Efficient methods for identifying mutated driver pathways in cancer. Bioinformatics 2012; 28:2940–2947 [CrossRef]
    [Google Scholar]
  35. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002; 30:1575–1584 [CrossRef]
    [Google Scholar]
  36. Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F et al. Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol 2019; 20:96 [CrossRef]
    [Google Scholar]
  37. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 2015; 38:237–245 [CrossRef]
    [Google Scholar]
  38. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T et al. Re-evaluating prokaryotic species. Nat Rev Microbiol 2005; 3:733–739 [CrossRef]
    [Google Scholar]
  39. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [CrossRef]
    [Google Scholar]
  40. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [CrossRef]
    [Google Scholar]
  41. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [CrossRef]
    [Google Scholar]
  42. Pineiro M, Stanton C. Probiotic bacteria: legislative framework-- requirements to evidence basis. J Nutr 2007; 137:850S–853 [CrossRef]
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. Schumann P. Peptidoglycan structure. Methods in Microbiology Elsevier; 2011 pp 101–129
    [Google Scholar]
  45. 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 [CrossRef]
    [Google Scholar]
  46. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [CrossRef]
    [Google Scholar]
  47. Biavati B, Mattarelli P. Genus Bifidobacterium. Bergey’s Manual of Systematic Bacteriology Springer-Verlag: New York Inc; 2012 pp 171–206
    [Google Scholar]
  48. Karp PD, Paley S, Romero P. The pathway tools software. Bioinformatics 2002; 18:S225–S232 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004032
Loading
/content/journal/ijsem/10.1099/ijsem.0.004032
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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