1887

Abstract

Strains LMG 1627, LMG 1636 and LMG 1637 were all isolated from cider fermentations in the 1940s and 1950s. A recent study based on MALDI-TOF MS and gene sequence analyses suggested they represented novel species. In the present study, we determined the whole-genome sequences of these strains and analysed their phenotypic and chemotaxonomic characteristics. A phylogenomic analysis based on 107 single-copy core genes revealed that they represented a single lineage with , , and , and with as an outgroup to this cluster. OrthoANIu value and dDDH analyses among these and other type strains confirmed that these three strains represented two novel species, which could be differentiated from other closely related type strains of by different phenotypic tests, such as ketogenesis from glycerol. We therefore propose to classify strain LMG 1627 in the novel species sp. nov., with LMG 1627 (=NCIMB 8945) as the type strain, and to classify strains LMG 1636 and LMG 1637 in the novel species sp. nov., with LMG 1636 (=NCIMB 8956) as the type strain.

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2020-10-14
2024-12-09
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References

  1. Crotti E, Rizzi A, Chouaia B, Ricci I, Favia G et al. Acetic acid bacteria, newly emerging symbionts of insects. Appl Environ Microbiol 2010; 76:6963–6970 [View Article][PubMed]
    [Google Scholar]
  2. De Roos J, De Vuyst L. Acetic acid bacteria in fermented foods and beverages. Curr Opin Biotechnol 2018; 49:115–119 [View Article][PubMed]
    [Google Scholar]
  3. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Germany Prokaryotic Nomenclature Up-to-date, [August, 2019].
  4. Trček J, Mahnič A, Rupnik M. Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing. Int J Food Microbiol 2016; 223:57–62 [View Article][PubMed]
    [Google Scholar]
  5. Skok B, Trček J. Comparison of cultivable acetic acid bacterial microbiota in organic and conventional apple cider vinegar. Food Technol Biotechnol 2016; 54:113–119 [View Article][PubMed]
    [Google Scholar]
  6. Shimwell JL, Carr JG. Old and new cellulose-producing acetobacter species. J Inst Brew 1958; 64:477–484 [View Article]
    [Google Scholar]
  7. Shimwell JL, Carr JG. Derivation of non-acetifying "quasiacetobacters" from a true Acetobacter strain, and vice versa. Antonie van Leeuwenhoek 1960; 26:169–181 [View Article][PubMed]
    [Google Scholar]
  8. Yamada Y. Transfer of Gluconacetobacter kakiaceti, Gluconacetobacter medellinensis and Gluconacetobacter maltaceti to the genus Komagataeibacter as Komagataeibacter kakiaceti comb. nov., Komagataeibacter medellinensis comb. nov. and Komagataeibacter maltaceti comb. nov. Int J Syst Evol Microbiol 2014; 64:1670–1672 [View Article][PubMed]
    [Google Scholar]
  9. Carr JG. Acetobacter estunense nov. spec., an addition to Frateur's ten basic species. Antonie van Leeuwenhoek 1958; 24:157–160 [View Article][PubMed]
    [Google Scholar]
  10. De Ley J. Comparative carbohydrate metabolism and a proposal for a phylogenetic relationship of the acetic acid bacteria. Microbiology 1961; 24:31–50
    [Google Scholar]
  11. Schell J, De Ley J. Variability of acetic acid bacteria. Antonie van Leeuwenhoek 1962; 28:445–465 [View Article][PubMed]
    [Google Scholar]
  12. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. Yoon SH, Ha SM, 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]
  15. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  16. Li L, Cleenwerck I, De Vuyst L, Vandamme P. Identification of acetic acid bacteria through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and report of Gluconobacter nephelii Kommanee et al. 2011 and Gluconobacter uchimurae Tanasupawat et al. 2012 as later heterotypic synonyms of Gluconobacter japonicus Malimas et al. 2009 and Gluconobacter oxydans (Henneberg 1897) de Ley 1961 (Approved Lists 1980) emend. Gosselé et al. 1983, respectively. Syst Appl Microbiol 2017; 40:123–134 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  19. Spitaels F, Li L, Wieme A, Balzarini T, Cleenwerck I et al. Acetobacter lambici sp. nov., isolated from fermenting lambic beer. Int J Syst Evol Microbiol 2014; 64:1083–1089 [View Article]
    [Google Scholar]
  20. 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]
  21. Spitaels F, Wieme A, Balzarini T, Cleenwerck I, Van Landschoot A et al. Gluconobacter cerevisiae sp. nov., isolated from the brewery environment. Int J Syst Evol Microbiol 2014; 64:1134–1141 [View Article][PubMed]
    [Google Scholar]
  22. Huang CH, Chang MT, Huang L, Chua WS. Molecular discrimination and identification of Acetobacter genus based on the partial heat shock protein 60 gene (hsp60) sequences. J Sci Food Agric 2014; 94:213–218 [View Article][PubMed]
    [Google Scholar]
  23. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
    [Google Scholar]
  24. Letunic I, Bork P. Interactive tree of life (iTOL) V4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article][PubMed]
    [Google Scholar]
  25. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  26. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  27. Edwards PR, Ewing WH. Identification of Enterobacteriaceae USA: Burgess Publishing Company; 1972
    [Google Scholar]
  28. Cleenwerck I, Vandemeulebroecke K, Janssens D, Swings J. Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 2002; 52:1551–1558 [View Article][PubMed]
    [Google Scholar]
  29. Asai T, Iizuka H, Komagata K. The flagellation and taxonomy of genera Gluconobacter and Acetobacter with reference to the existence of intermediate strains. J Gen Appl Microbiol 1964; 10:95–126 [View Article]
    [Google Scholar]
  30. Spitaels F, Li L, Wieme A, Balzarini T, Cleenwerck I et al. Acetobacter lambici sp. nov., isolated from fermenting lambic beer. Int J Syst Evol Microbiol 2014; 64:1083–1089 [View Article][PubMed]
    [Google Scholar]
  31. Gosselé F, Swings J, De Ley J. A rapid, simple and simultaneous detection of 2-keto-, 5-keto-and 2,5-diketogluconic acids by thin-layer chromatography in culture media of acetic acid bacteria. Zentralblatt für Bakteriologie: I. Abt. Originale C: Allgemeine, angewandte und ökologische Mikrobiologie 1980; 1:178–181 [View Article]
    [Google Scholar]
  32. Lambert B, Kersters K, Gosselé F, Swings J, De Ley J. Gluconobacters from honey bees. Antonie van Leeuwenhoek 1981; 47:147–157 [View Article][PubMed]
    [Google Scholar]
  33. Swings J. Phenotypic identification of acetic acid bacteria.. Identification Methods in Applied and Environmental Microbiology (The Society for Applied Bacteriology Technical Series no 29). 1992 pp 103–110
    [Google Scholar]
  34. Pitiwittayakul N, Theeragool G, Yukphan P, Chaipitakchonlatarn W, Malimas T et al. Acetobacter suratthanensis sp. nov., an acetic acid bacterium isolated in Thailand. Ann Microbiol 2016; 66:1157–1166 [View Article]
    [Google Scholar]
  35. Li L, Wieme A, Spitaels F, Balzarini T, Nunes OC et al. Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis. Int J Syst Evol Microbiol 2014; 64:2407–2415 [View Article][PubMed]
    [Google Scholar]
  36. Dumolin C, Aerts M, Verheyde B, Schellaert S, Vandamme T et al. Introducing SPeDE: high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption–ionization Time of flight mass spectrometry data. mSystems 2019; 4:e00437–00419 [View Article][PubMed]
    [Google Scholar]
  37. Ferrer S, Mañes-Lázaro R, Benavent-Gil Y, Yépez A, Pardo I. Acetobacter musti sp. nov., isolated from Bobal grape must. Int J Syst Evol Microbiol 2016; 66:957–961 [View Article][PubMed]
    [Google Scholar]
  38. Strohalm M, Kavan D, Novák P, Volný M, Havlícek V. mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data. Anal Chem 2010; 82:4648–4651 [View Article][PubMed]
    [Google Scholar]
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