1887

Abstract

Four strains of members of the genus were isolated from samples associated with the western honey bee , which could not be assigned to a species with a validly published name. Strains TMW 2.2543, TMW 2.2556, TMW 2.2558 and TMW 2.2559 exhibit DNA–DNA hybridisation (isDDH) and orthologous average nucleotide identity (orthoANI) values below species delineation thresholds compared with all described species of the genus and with each other. TMW 2.2556 and TMW 2.2558 form their own clade within the genus. The major respiratory quinone of all strains was Q-10. The composition of cellular fatty acids was diverse between strains. All strains stained Gram-negative, were rod-shaped, strictly aerobic, pellicle-forming, catalase-positive, oxidase-negative, mesophilic and grew over a wide pH range; they were halosensitive but glucose-tolerant. Unlike the other studied strains, TMW 2.2558 was non-motile. Phylogenetic, chemotaxonomic and physiological analyses revealed a clear distinction between all the strains and species with validly published names. All the data support the proposition of four novel species within the genus , namely sp. nov., sp. nov., sp. nov. and sp. nov., with the respective type strains sp. nov. TMW 2.2543 (= DSM 114872, = LMG 32791), sp. nov. TMW 2.2556 (= DSM 114874, = LMG 32792), sp. nov. TMW 2.2558 (= DSM 114875, = LMG 32793) and sp. nov. TMW 2.2559 (= DSM 114877, = LMG 32794). Moreover, three genomes available in the NCBI database that have not yet been described as species with validly published names could be assigned to the proposed species. sp. ESL0378 and sp. ESL0385 to sp. nov. and sp. AS1 to sp. nov.

Funding
This study was supported by the:
  • Bundesministerium für Bildung und Forschung (Award FKZ 031A533)
    • Principle Award Recipient: NotApplicable
  • Bundesministerium für Wirtschaft und Technologie (Award AiF 21311 N)
    • Principle Award Recipient: LucaHärer
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005927
2023-06-20
2024-06-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/6/ijsem005927.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005927&mimeType=html&fmt=ahah

References

  1. Li L, Praet J, Borremans W, Nunes OC, Manaia CM et al. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop. Int J Syst Evol Microbiol 2015; 65:267–273 [View Article] [PubMed]
    [Google Scholar]
  2. Härer L, Hilgarth M, Ehrmann MA. Comparative genomics of acetic acid bacteria within the genus Bombella in light of beehive habitat adaptation. Microorganisms 2022; 10:1058 [View Article] [PubMed]
    [Google Scholar]
  3. Parish AJ, Rice DW, Tanquary VM, Tennessen JM, Newton ILG. Honey bee symbiont buffers larvae against nutritional stress and supplements lysine. ISME J 2022; 16:2160–2168 [View Article] [PubMed]
    [Google Scholar]
  4. Miller DL, Smith EA, Newton ILG, Graf J. A bacterial symbiont protects honey bees from fungal disease. mBio 2021; 12:e0050321 [View Article] [PubMed]
    [Google Scholar]
  5. Yun J-H, Lee J-Y, Hyun D-W, Jung M-J, Bae J-W. Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee. Int J Syst Evol Microbiol 2017; 67:2184–2188 [View Article] [PubMed]
    [Google Scholar]
  6. Hilgarth M, Redwitz J, Ehrmann MA, Vogel RF, Jakob F. Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  7. Smith EA, Anderson KE, Corby-Harris V, McFrederick QS, Parish AJ et al. Reclassification of seven honey bee symbiont strains as Bombella apis. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  8. Bonilla-Rosso G, Paredes Juan C, Das S, Ellegaard KM, Emery O et al. Acetobacteraceae in the honey bee gut comprise two distant clades with diverging metabolism and ecological niches. Genomics [View Article]
    [Google Scholar]
  9. Huptas C, Scherer S, Wenning M. Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly. BMC Res Notes 2016; 9:269 [View Article] [PubMed]
    [Google Scholar]
  10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  11. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. 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 [View Article] [PubMed]
    [Google Scholar]
  14. Kumar S, Stecher G, Li M, Knyaz C, Tamura K et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  15. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F-J et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154 [View Article]
    [Google Scholar]
  16. Dieckmann MA, Beyvers S, Nkouamedjo-Fankep RC, Hanel PHG, Jelonek L et al. EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Nucleic Acids Res 2021; 49:W185–W192 [View Article] [PubMed]
    [Google Scholar]
  17. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
    [Google Scholar]
  18. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  20. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  21. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  22. Song W, Sun H-X, Zhang C, Cheng L, Peng Y et al. Prophage hunter: an integrative hunting tool for active prophages. Nucleic Acids Res 2019; 47:W74–W80 [View Article] [PubMed]
    [Google Scholar]
  23. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article] [PubMed]
    [Google Scholar]
  24. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  25. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  26. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  27. 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 [View Article] [PubMed]
    [Google Scholar]
  28. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article] [PubMed]
    [Google Scholar]
  29. Aydin YA, Aksoy ND. Isolation of cellulose producing bacteria from wastes of vinegar fermentation. WCECS 2009; 1:
    [Google Scholar]
  30. Shimwell JL. The true significance of Hoyer's medium in the differentiation of Acetobacter species. J Inst Brew 1957; 63:44–45 [View Article]
    [Google Scholar]
  31. Shimwell JL, Carr JG, Rhodes ME. Differentiation of Acetomonas and Pseudomonas. J Gen Microbiol 1960; 23:283–286 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005927
Loading
/content/journal/ijsem/10.1099/ijsem.0.005927
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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