1887

Abstract

Two bacterial strains, isolates AC10 and AC20, which were reported in a previous study on the diversity of acetic acid bacteria in Thailand, were subjected to a taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the two isolates were located closely to the type strains of and . However, the two isolates formed a separate cluster from the type strains of the two species. The genomic DNA of isolate AC10 was sequenced. The assembled genomes of the isolate were analysed for average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). The results showed that the highest ANI and dDDH values between isolate AC10 and DSM 3503 were 91.15 and 68.2 %, which are lower than the suggested values for species delineation. The genome-based tree was reconstructed and the phylogenetic lineage based on genome sequences showed that the lineage of isolate AC10 was distinct from DSM 3503 and its related species. The two isolates were distinguished from and their relatives by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, AC10 (=BCC 15749=TBRC 11329=NBRC 103576) and AC20 (=BCC 15759=TBRC 11330=NBRC 103579), can be assigned to an independent species within the genus , and the name sp. nov. is proposed for the two isolates.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004292
2020-06-25
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4351.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004292&mimeType=html&fmt=ahah

References

  1. Komagata K, Iino T, Yamada Y. The Family Acetobacteraceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Heidelberg: Springer Berlin Heidelberg; 2014 pp 3–78
    [Google Scholar]
  2. Malimas T, Vu HTL, Muramatsu Y, Yukphan P, Tanasupawat S. Systematics of acetic acid bacteria. In Sengun IY. editor Acetic Acid Bacteria: Fundamental and Food Application CRC Press; 2017 pp 3–43
    [Google Scholar]
  3. Oren A, Garrity G. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:3313–3314 [View Article][PubMed]
    [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  5. Katsura K, Yamada Y, Uchimura T, Komagata K. Gluconobacter asaii Mason and Claus 1989 is a junior subjective synonym of Gluconobacter cerinus Yamada and Akita 1984. Int J Syst Evol Microbiol 2002; 52:1635–1640 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Muramatsu Y, Yukphan P, Takahashi M, Kaneyasu M, Malimas T et al. 16S rRNA gene sequences analysis of acetic acid bacteria isolated from Thailand. Microbiology and Culture Collections 2009; 25:13–20
    [Google Scholar]
  8. Yamada Y, Hosono R, Lisdyanti P, Widyastuti Y, Saono S et al. Identification of acetic acid bacteria isolated from Indonesian sources, especially of isolates classified in the genus Gluconobacter . J Gen Appl Microbiol 1999; 45:23–28 [View Article][PubMed]
    [Google Scholar]
  9. Yamada Y, Katsura K, Kawasaki H, Widyastuti Y, Saono S et al. Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the alpha-Proteobacteria . Int J Syst Evol Microbiol 2000; 50:823–829 [View Article][PubMed]
    [Google Scholar]
  10. Yamada Y, Okada Y, Kondo K. Isolation and characterization of "polarly flagellated intermediate strains" in acetic acid bacteria. J Gen Appl Microbiol 1976; 22:237–245 [View Article]
    [Google Scholar]
  11. Yukphan P, Potacharoen W, Tanasupawat S, Tanticharoen M, Yamada Y. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria . Int J Syst Evol Microbiol 2004; 54:313–316 [View Article][PubMed]
    [Google Scholar]
  12. Ezaki T, Yamamoto N, Ninomiya K, Suzuki S, Yabuuchi E. Transfer of Peptococcus indolicus, Peptococcus asaccharolyticus, Peptococcus prevotii, and Peptococcus magnus to the Genus Peptostreptococcus and Proposal of Peptostreptococcus tetradius sp. nov. Int J Syst Bacteriol 1983; 33:683–698 [View Article]
    [Google Scholar]
  13. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [Google Scholar]
  14. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article][PubMed]
    [Google Scholar]
  15. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBio-Cloud: 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]
  16. Kim M, Oh H-S, Park S-C, 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]
  17. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  18. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
    [Google Scholar]
  19. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  25. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 2016; 44:W3–W10 [View Article][PubMed]
    [Google Scholar]
  26. Andrews S. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc ; 2010
  27. Krueger F. Trim galore!: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ; 2015
  28. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article]
    [Google Scholar]
  31. 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]
    [Google Scholar]
  32. 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]
    [Google Scholar]
  33. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  34. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article]
    [Google Scholar]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  36. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article][PubMed]
    [Google Scholar]
  37. Malimas T, Yukphan P, Takahashi M, Muramatsu Y, Kaneyasu M et al. Gluconobacter roseus (ex Asai 1935) sp. nov., nom. rev., a pink-colored acetic acid bacterium in the Alphaproteobacteria . J Gen Appl Microbiol 2008; 54:119–125 [View Article][PubMed]
    [Google Scholar]
  38. Malimas T, Yukphan P, Takahashi M, Muramatsu Y, Kaneyasu M et al. Gluconobacter sphaericus (Ameyama 1975) comb. nov., a brown pigment-producing acetic acid bacterium in the Alphaproteobacteria . J Gen Appl Microbiol 2008; 54:211–220 [View Article][PubMed]
    [Google Scholar]
  39. 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]
  40. Malimas T, Yukphan P, Takahashi M, Kaneyasu M, Potacharoen W et al. Gluconobacter kondonii sp. nov., an acetic acid bacterium in the alpha-Proteobacteria . J Gen Appl Microbiol 2007; 53:301–307 [View Article][PubMed]
    [Google Scholar]
  41. Mason LM, Claus GW. Phenotypic characteristics correlated with deoxyribonucleic acid sequence similarities for three species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961, G. frateurii sp. nov., and G. asaii sp. nov. Int J Syst Bacteriol 1989; 39:174–184 [View Article]
    [Google Scholar]
  42. Yamada Y, Aida K, Ocirc UT. Enzymatic studies on the oxidation of sugar and sugar alcohol. V. Ubiquinone of acetic acid bacteria and its relation to classification of Gluconobacter and Acetobacter, especially of the so-called intermediate strains. J Gen App Microbiol 1969; 15:181–196 [View Article]
    [Google Scholar]
  43. 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]
  44. 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]
  45. Yukphan P, Malimas T, Lundaa T, Muramatsu Y, Takahashi M et al. Gluconobacter wancherniae sp. nov., an acetic acid bacterium from Thai isolates in the alpha-Proteobacteria . J Gen Appl Microbiol 2010; 56:67–73 [View Article][PubMed]
    [Google Scholar]
  46. Malimas T, Yukphan P, Takahashi M, Muramatsu Y, Kaneyasu M et al. Gluconobacter japonicus sp. nov., an acetic acid bacterium in the Alphaproteobacteria . Int J Syst Evol Microbiol 2009; 59:466–471 [View Article][PubMed]
    [Google Scholar]
  47. Malimas T, Yukphan P, Lundaa T, Muramatsu Y, Takahashi M et al. Gluconobacter kanchanaburiensis sp. nov., a brown pigment-producing acetic acid bacterium for Thai isolates in the Alphaproteobacteria . J Gen Appl Microbiol 2009; 55:247–254 [View Article][PubMed]
    [Google Scholar]
  48. Vu HTL, Yukphan P, Chaipitakchonlatarn W, Malimas T, Muramatsu Y et al. Nguyenibacter vanlangensis gen. nov., sp. nov., an unusual acetic acid bacterium in the α-Proteobacteria . J Gen Appl Microbiol 2013; 59:153–166 [View Article][PubMed]
    [Google Scholar]
  49. Matsuda N, Matsuda M, Notake S, Yokokawa H, Kawamura Y et al. Evaluation of a simple protein extraction method for species identification of clinically relevant staphylococci by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 50:3862–3866 [View Article][PubMed]
    [Google Scholar]
  50. Wu L, McCluskey K, Desmeth P, Liu S, Hideaki S et al. The global Catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species. Gigascience 2018; 7:1–4 [View Article][PubMed]
    [Google Scholar]
  51. Yukphan P, Takahashi M, Potacharoen W, Tanasupawat S, Nakagawa Y et al. Gluconobacter albidus (ex Kondo and Ameyama 1958) sp. nov., nom. rev., an acetic acid bacterium in the alpha-Proteobacteria . J Gen Appl Microbiol 2004; 50:235–242 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004292
Loading
/content/journal/ijsem/10.1099/ijsem.0.004292
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