1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 12

Bifidobacteria in two-toed sloths (): phylogenetic characterization of the novel taxon sp. nov. Free

Abstract

Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth () housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (60, B, C, J, G) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of subsp. DSM 21854 (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6), whereas the type strain of DSM 20436 (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6 and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6 combined with phenotypic analyses clearly revealed that the strain BRDM 6 represents a novel species for which the names sp. nov. (BRDM 6=NBRC 114053=BCRC 81222) is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bifidobacterium , Bifidobacterium choloepi , Choloepus didactylus , new species and two-toed sloth
Funding
This study was supported by the:
  • JSPS KAKENHI (Award 17K19248)
    • Principle Award Recipient: Masanori Arita
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004506
2020-10-14
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6115.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004506&mimeType=html&fmt=ahah

References

  1. Vendl C, Frei S, Dittmann MT, Furrer S, Osmann C et al. Digestive physiology, metabolism and methane production of captive Linné's two-toed sloths (Choloepus didactylus). J Anim Physiol Anim Nutr 2016; 100:552–564 [View Article][PubMed]
     [Google Scholar]
  2. Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 2016; 18:1391–1402 [View Article][PubMed]
     [Google Scholar]
  3. Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A et al. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol 2014; 23:1301–1317 [View Article][PubMed]
     [Google Scholar]
  4. 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]
  5. Modesto M, Puglisi E, Bonetti A, Michelini S, Spiezio C et al. Bifidobacterium primatium sp. nov., Bifidobacterium scaligerum sp. nov., Bifidobacterium felsineum sp. nov. and Bifidobacterium simiarum sp. nov.: four novel taxa isolated from the faeces of the cotton top tamarin (Saguinus oedipus) and the emperor tamarin (Saguinus imperator). Syst Appl Microbiol 2018; 41:593–603 [View Article][PubMed]
     [Google Scholar]
  6. 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; 11:28342847 [View Article][PubMed]
     [Google Scholar]
  7. 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 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article][PubMed]
     [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 [View Article][PubMed]
     [Google Scholar]
  10. 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]
  11. D'Aimmo MR, Modesto M, Mattarelli P, Biavati B, Andlid T. Biosynthesis and cellular content of folate in bifidobacteria across host species with different diets. Anaerobe 2014; 30:169–177 [View Article][PubMed]
     [Google Scholar]
  12. Baffoni L, Stenico V, Strahsburger E, Gaggìa F, Di Gioia D et al. Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment. BMC Microbiol 2013; 13:149 [View Article][PubMed]
     [Google Scholar]
  13. Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LMT. 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 mida). Syst Appl Microbiol 2012; 35:92–97 [View Article][PubMed]
     [Google Scholar]
  14. 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 [View Article][PubMed]
     [Google Scholar]
  15. Ventura M, Canchaya C, Casale AD, 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]
  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. 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 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Mattarelli P, Holzapfel W, Franz C, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article][PubMed]
     [Google Scholar]
  20. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article][PubMed]
     [Google Scholar]
  23. Letunic I, Bork P. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  26. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
     [Google Scholar]
  27. Scardovi V. Genus Bifidobacterium . In Sneath PHA, Mair MES NS. (editors) Bergey’s Manual of Systematic Bacteriology Baltimore: 1986 pp 1418–1434
     [Google Scholar]
  28. Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S et al. Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2014; 64:2819–2827 [View Article][PubMed]
     [Google Scholar]
  29. Duranti S, Lugli GA, Viappiani A, Mancabelli L, Alessandri G et al. Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov. Int J Syst Evol Microbiol 2020; 70:2288–2297 [View Article][PubMed]
     [Google Scholar]
  30. Hamada M, Yamamura H, Komukai C, Tamura T, Suzuki K et al. Luteimicrobium album sp. nov., a novel actinobacterium isolated from a lichen collected in Japan, and emended description of the genus Luteimicrobium . J Antibiot 2012; 65:427–431 [View Article][PubMed]
     [Google Scholar]
  31. Nozawa Y, Sakai N, Arai K, Kawasaki Y, Harada K. Reliable and sensitive analysis of amino acids in the peptidoglycan of actinomycetes using the advanced Marfey's method. J Microbiol Methods 2007; 70:306–311 [View Article][PubMed]
     [Google Scholar]
  32. Morita H, Nakano A, Onoda H, Toh H, Oshima K et al. Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces. Int J Syst Evol Microbiol 2011; 61:2610–2615 [View Article][PubMed]
     [Google Scholar]
  33. Lauer E. Bifidobacterium gallicum sp. nov. isolated from human feces. Int J Syst Bacteriol 1990; 40:100–102 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004506
Loading
Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov.
Int J Syst Evol Microbiol 70, 6115 (2020); https://doi.org/10.1099/ijsem.0.004506
/content/journal/ijsem/10.1099/ijsem.0.004506
/content/journal/ijsem/10.1099/ijsem.0.004506
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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