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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 4

sp. nov. isolated from fermented vegetable residue No Access

Abstract

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive fermentative bacterium, designated strain CC-MHH1034, isolated from a fermented vegetable residue. Cells of strain CC-MHH1034 were facultatively anaerobic, non-motile, and non-spore-forming rods, exhibiting positive catalase, oxidase and protease activities. Optimal growth occurred at 30 °С and pH 6.0. Strain CC-MHH1034 shared the highest 16S rRNA gene sequence similarities with (95.9 %) followed by (95.1 %) and established a distinct taxonomic lineage associated with these species. Highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-MHH1034 versus (71.1–71.6 %, =2) followed by (66.5–66.8 %, =2), (64.1–65.8 %, =4). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-MHH1034 against was 19.2–19.5 % (=2). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, four unidentified glycolipids, four unidentified phospholipids and one unidentified lipid. The major polyamine was -homospermidine and -diaminopimelic acid was detected as the cell-wall peptidoglycan. The dominating cellular fatty acids (>5 %) included C, -C, -C and C 9c. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH, and the phylogenomic placement, strain CC-MHH1034 is considered to represent a novel species of the genus , affiliated to the family , for which the name sp. nov. is proposed. The type strain is CC-MHH1034 (=BCRC 81220=JCM 33476).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Agrilactobacillus fermenti , orthologous average nucleotide identity (OrthoANI) and polyphasic taxonomic approach
Funding
This study was supported by the:
  • Ministry of Science and Technology, Taiwan (Award MOST 110-2811-B-005-018)
    • Principle Award Recipient: YoungChiu-Chung
  • Ministry of Science and Technology, Taiwan (Award MOST 110-2811-B-005-018)
    • Principle Award Recipient: TsaiChia-Fang
  • Ministry of Science and Technology, Taiwan (Award MOST 110-2811-B-005-018)
    • Principle Award Recipient: LinShih-Yao
© 2022 The Authors
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References

  1. Beijerinck M, Anhäufungsversuche MIT. Ureumbakterien. Ureumspaltung durch urease und durch Katabolismus. Zentralbl Bakteriol Parasitenkd Infekt Hyg II Abt 1901; 7:33–61
     [Google Scholar]
  2. Zheng J, Wittouck S, Salvetti E, Franz C, Harris HMB et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article] [PubMed]
     [Google Scholar]
  3. 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]
  4. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [View Article] [PubMed]
     [Google Scholar]
  5. Endo A, Okada S. Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue. Int J Syst Evol Microbiol 2007; 57:870–872 [View Article] [PubMed]
     [Google Scholar]
  6. Wei YX, Gu CT. Lactobacillus yilanensis sp. nov., Lactobacillus bayanensis sp. nov., Lactobacillus keshanensis sp. nov., Lactobacillus kedongensis sp. nov., Lactobacillus baiquanensis sp. nov., Lactobacillus jidongensis sp. nov., Lactobacillus hulinensis sp. nov., Lactobacillus mishanensis sp. nov. and Lactobacillus zhongbaensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 2019; 69:3178–3190 [View Article]
     [Google Scholar]
  7. Manes-Lazaro R, Ferrer S, Rossello-Mora R, Pardo I. Lactobacillus oeni sp. nov., from wine. Int J Syst Evol Microbiol 2009; 59:2010–2014 [View Article] [PubMed]
     [Google Scholar]
  8. Fujisawa T, Shirasaka S, Watabe J, Mitsuoka T. Lactobacillus aviarius sp. nov.: a new species isolated from the intestine of chickens. Syst Appl Microbiol 1984; 5:414–420 [View Article]
     [Google Scholar]
  9. Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y et al. Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers. Int J Syst Evol Microbiol 2011; 61:1356–1359 [View Article] [PubMed]
     [Google Scholar]
  10. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 32–34
     [Google Scholar]
  11. 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]
  12. Lin S-Y, Liu Y-C, Hameed A, Hsu Y-H, Lai W-A et al. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 2013; 63:3762–3768 [View Article] [PubMed]
     [Google Scholar]
  13. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int J Syst Evol Microbiol 2014; 64:138–145 [View Article]
     [Google Scholar]
  14. Lin SY, Hameed A, Tsai CF, Young CC. Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field. Antonie van Leeuwenhoek 2021; 114:2101–2111 [View Article] [PubMed]
     [Google Scholar]
  15. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
     [Google Scholar]
  16. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA using BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article] [PubMed]
     [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  23. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. eds Mammalian Protein Metabolism vol 3 New York: Academic Press; 1969 pp 21–32
     [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. 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 Bacteriol 1994; 44:846–849 [View Article]
     [Google Scholar]
  26. 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]
  27. 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]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervalsand improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  29. de Lajudie PM, Young JPW. International committee on systematics of prokaryotes subcommittee for the taxonomy of rhizobium and agrobacterium minutes of the meeting. Int J Syst Evol Microbiol 2017; 67:2485–2494 [View Article] [PubMed]
     [Google Scholar]
  30. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article] [PubMed]
     [Google Scholar]
  31. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  32. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  33. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:002195 [View Article] [PubMed]
     [Google Scholar]
  34. Katoh K, Standley DM. MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  35. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxyl acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
     [Google Scholar]
  38. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
     [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
  40. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article] [PubMed]
     [Google Scholar]
  41. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  42. Rhuland LE, Work E, Denman RF, Hoare DS. The behavior of the isomers of diaminopimelic acid on paper chromatograms. J Am Chem Soc 2002; 77:4844–4846 [View Article]
     [Google Scholar]
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Agrilactobacillus fermenti sp. nov. isolated from fermented vegetable residue
Int J Syst Evol Microbiol 72, 005336 (2022); https://doi.org/10.1099/ijsem.0.005336
/content/journal/ijsem/10.1099/ijsem.0.005336
/content/journal/ijsem/10.1099/ijsem.0.005336
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