1887

Abstract

A novel bifidobacteria (designated S053-2) was isolated from the gut of honeybee (). Strain S053-2 was characterized using a polyphasic taxonomic approach. The result of 16S rRNA gene sequence analysis indicated that strain S053-2 was phylogenetically related to the type strains of , , , , , , and , and had 95.5–99.7 % 16S rRNA gene sequence similarities. Based on the 16S rRNA gene sequence analysis, strain S053-2 was most closely related to the type strain of , having 99.7 % 16S rRNA gene sequence similarity. Strain S053-2 had relatively low (91.6–95.7 %) , , , , , , , , , and sequence similarities to the type strain of . Strain S053-2 had 94.5–95.3% , , , and sequence similarities to the type strain of . The phylogenomic tree indicated that strain S053-2 belonged to the group, and was most closely related to the type strains of , , and , and distantly related to type strains of other phylogenetically related species in the group. Strain S053-2 shared the highest average nucleotide identity (ANI, 93.8 %), digital DNA–DNA hybridization (dDDH, 52.4 %) and average amino acid identity (AAI, 95.6%) values with W8102. Strain S053-2 shared 91.1 % ANI, 41.9 % dDDH and 92.5 % AAI values with DSM 20089. Acid production from -arabinose, -xylose, -mannose, amygdalin, cellobiose, maltose, melibiose, sucrose, raffinose, gentiobiose and -fucose, and activity of esterase lipase (C8) and -fucosidase could differentiate strain S053-2 from DSM 20089. Acid production from -mannose, maltose, sucrose, melezitose and gentiobiose, and activity of -fucosidase could differentiate strain S053-2 from W8102. Based upon the data obtained in the present study, a novel species, sp. nov., is proposed, and the type strain is S053-2 (=JCM 34710=CCTCC AB 2021129).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award no. 31471594)
    • Principle Award Recipient: ChunTao Gu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005390
2022-05-24
2022-07-04
Loading full text...

Full text loading...

References

  1. Li TT, Zhang HX, Gu CT. Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Aapis mellifera) Figshare 2022 DOI: 10.6084/m9.figshare.19425983.v1
    [Google Scholar]
  2. Neuzil-Bunesova V, Lugli GA, Modrackova N, Vlkova E, Bolechova P et al. Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: Bifidobacterium erythrocebi sp. nov., Bifidobacterium moraviense sp. nov., Bifidobacterium oedipodis sp. nov., Bifidobacterium olomucense sp. nov. and Bifidobacterium panos sp. nov. Int J Syst Evol Microbiol 2021; 71:004573 [View Article]
    [Google Scholar]
  3. Modesto M, Satti M, Watanabe K, Huang C-H, Liou J-S et al. Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov. Int J Syst Evol Microbiol 2020; 70:6115–6125 [View Article] [PubMed]
    [Google Scholar]
  4. 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]
  5. Chen J, Wang J, Zheng H. Characterization of Bifidobacterium apousia sp. nov., Bifidobacterium choladohabitans sp. nov., and Bifidobacterium polysaccharolyticum sp. nov., three novel species of the genus Bifidobacterium from honey bee gut. Syst Appl Microbiol 2021; 44:126247 [View Article]
    [Google Scholar]
  6. Lugli GA, Calvete-Torre I, Alessandri G, Milani C, Turroni F et al. Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov. Syst Appl Microbiol 2021; 44:126273 [View Article]
    [Google Scholar]
  7. Li TT, Liu DD, Fu ML, Gu CT. Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera). Int J Syst Evol Microbiol 2020; 70:3123–3133 [View Article]
    [Google Scholar]
  8. An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043–2048 [View Article] [PubMed]
    [Google Scholar]
  9. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  10. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 1989; 29:170–179 [View Article] [PubMed]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  12. 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 [View Article] [PubMed]
    [Google Scholar]
  13. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article] [PubMed]
    [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  15. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  16. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Neuzil-Bunesova V, Lugli GA, Modrackova N, Makovska M, Mrazek J et al. Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris). Int J Syst Evol Microbiol 2020; 70:5040–5047 [View Article] [PubMed]
    [Google Scholar]
  19. Ventura M, Zink R. Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl Environ Microbiol 2003; 69:7517–7522 [View Article] [PubMed]
    [Google Scholar]
  20. Ventura M, Zink R, Fitzgerald GF, van Sinderen D. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl Environ Microbiol 2005; 71:487–500 [View Article] [PubMed]
    [Google Scholar]
  21. Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J. Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie van Leeuwenhoek 2019; 112:1785–1800 [View Article] [PubMed]
    [Google Scholar]
  22. Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713–721 [View Article] [PubMed]
    [Google Scholar]
  23. Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z et al. Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol 2020; 65:143–151 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
    [Google Scholar]
  26. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  27. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  28. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  29. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
    [Google Scholar]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  32. Modesto M, Checcucci A, Mattarelli P. Identification of Bifidobacteria by the phosphoketolase assay. Methods Mol Biol 2021; 2278:141–148 [View Article] [PubMed]
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE, USA: Microbial ID Inc; 1990
  34. 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 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005390
Loading
/content/journal/ijsem/10.1099/ijsem.0.005390
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare

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