1887

Abstract

A Gram-stain-negative, obligately aerobic bacterium, designated strain B6, was isolated from rice wine vinegar in the Republic of Korea. Cells were non-motile and oval short rods showing catalase-positive and oxidase-negative activities. Growth was observed at 15–45 °C (optimum, 30 °C) and pH 3.5–8.0 (optimum, pH 5.5–6.5). Strain B6 contained summed feature 8 (comprising Cω7 and/or C 6), and C as major fatty acids and ubiquinone-9 was identified as the sole isoprenoid quinone. The G+C content of the genomic DNA calculated from the whole genome was 53.1 mol%. Strain B6 was most closely related to LMG 1262 with very high 16S rRNA gene sequence similarity (100 %) and the strains formed a very close phylogenetic lineage together in phylogenetic trees based on 16S rRNA gene sequences. However, relatedness analyses based on concatenated amino acid sequences of 354 core genes and whole-cell MALDI-TOF profiles showed that strain B6 may form a distinct phyletic lineage from species. In addition, average nucleotide identity and DNA–DNA hybridization values between strain B6 and the type strains of species were less than 93.3 and 51.4 %, respectively. The genomic features of strain B6 were also differentiated from those of closely related type strains. Based on the phenotypic, chemotaxonomic and genomic features, strain B6 clearly represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is B6 (=KACC 21201=JCM 33371).

Funding
This study was supported by the:
  • National Institute of Biological Resources (Award NIBR No. 2019-02-001)
    • Principle Award Recipient: Che Ok Jeon
  • National Research Foundation of Korea (Award 2017M3C1B5019250)
    • Principle Award Recipient: Che Ok Jeon
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2020-01-29
2024-03-29
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References

  1. Yamada Y, Yukphan P. Genera and species in acetic acid bacteria. Int J Food Microbiol 2008; 125:15–24 [View Article]
    [Google Scholar]
  2. Cleenwerck I, Gonzalez A, Camu N, Engelbeen K, De Vos P et al. Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation. Int J Syst Evol Microbiol 2008; 58:2180–2185 [View Article]
    [Google Scholar]
  3. Iino T, Suzuki R, Kosako Y, Ohkuma M, Komagata K et al. Acetobacter okinawensis sp. nov., Acetobacter papayae sp. nov., and Acetobacter persicus sp. nov.; novel acetic acid bacteria isolated from stems of sugarcane, fruits, and a flower in Japan. J Gen Appl Microbiol 2012; 58:235–243 [View Article]
    [Google Scholar]
  4. Chakravorty S, Bhattacharya S, Chatzinotas A, Chakraborty W, Bhattacharya D et al. Kombucha tea fermentation: microbial and biochemical dynamics. Int J Food Microbiol 2016; 220:63–72 [View Article]
    [Google Scholar]
  5. 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]
  6. 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]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. 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]
  9. Kim KH, Cho GY, Chun BH, Weckx S, Moon JY et al. Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobacter ascendens sp. nov., comb. nov. Syst Appl Microbiol 2018; 41:324–332 [View Article]
    [Google Scholar]
  10. Sievers M, Swings J. Acetobacter . In Bergey’s Manual of Of Systematics of Archaea and Bacteria 2015
    [Google Scholar]
  11. Khan SA, Jeong SE, Jung HS, Quan Z-X, Jeon CO. Roseicella frigidaeris gen. nov., sp. nov., isolated from an air-conditioning system. Int J Syst Evol Microbiol 2019; 69:1384–1389 [View Article]
    [Google Scholar]
  12. 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]
    [Google Scholar]
  13. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [View Article]
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. Sambrook J, Russell DW. Molecular Cloning: a Laboratory Manual, 3rd edition. UK: Coldspring-Harbour Laboratory Press; 2001
    [Google Scholar]
  16. 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]
    [Google Scholar]
  17. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article]
    [Google Scholar]
  18. 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]
    [Google Scholar]
  19. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article]
    [Google Scholar]
  20. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  26. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–W57 [View Article]
    [Google Scholar]
  27. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
    [Google Scholar]
  28. Jones P, Binns D, Chang H-Y, Fraser M, Li W et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014; 30:1236–1240 [View Article]
    [Google Scholar]
  29. Jia B, Chun BH, Cho GY, Kim KH, Moon JY et al. Complete genome sequences of two acetic acid-producing Acetobacter pasteurianus Strains (Subsp. ascendens LMG 1590T and Subsp. paradoxus LMG 1591T). Front Bioeng Biotechnol 2017; 5:33 [View Article]
    [Google Scholar]
  30. Chinnawirotpisan P, Theeragool G, Limtong S, Toyama H, Adachi OO et al. Quinoprotein alcohol dehydrogenase is involved in catabolic acetate production, while NAD-dependent alcohol dehydrogenase in ethanol assimilation in Acetobacter pasteurianus SKU1108. J Biosci Bioeng 2003; 96:564–571 [View Article]
    [Google Scholar]
  31. Wang B, Shao Y, Chen T, Chen W, Chen F. Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics. Sci Rep 2015; 5:18330 [View Article]
    [Google Scholar]
  32. Marshall BJ, Barrett LJ, Prakash C, McCallum RW, Guerrant RL. Urea protects Helicobacter (Campylobacter) pylori from the bactericidal effect of acid. Gastroenterology 1990; 99:697–702 [View Article]
    [Google Scholar]
  33. Gomori G. Preparation of buffers for use in enzyme studies. In Colowick SP, Kaplan NO. (editors) Methods in enzymology New York: Academic Press; 1955 pp 138–146
    [Google Scholar]
  34. Krisch J, Szajani B. Ethanol and acetic acid tolerance in free and immobilized cells of Saccharomyces cerevisiae and Acetobacter aceti . Biotechnol Lett 1997; 19:525–528 [View Article]
    [Google Scholar]
  35. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. editor Methods for general and molecular bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  36. Gosselé F, Swings J, De Ley J, A rapid DLJ. 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]
  37. 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]
    [Google Scholar]
  38. 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]
  39. Jeon JH, Oh H-W, Yun CS, Byun B-K, Park J-J et al. Rapid and reliable species identification of Carposina sasakii from its morphological homologues, by MALDI-TOF mass spectrometry. J Asia Pac Entomol 2017; 20:411–415 [View Article]
    [Google Scholar]
  40. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–208
    [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids; 1990
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