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Volume 72, Issue 12

sp. nov. and sp. nov., isolated from traditional Chinese pickle No Access

Abstract

Two Gram-stain-positive bacterial strains, designated 213-9(3) and 30-1(2), were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain 213-9(3) was most closely related to TMW 1.1424, 151-2B and 220-4, having 99.7–99.9 % 16S rRNA gene sequence similarities; strain 30-1(2) was most closely related to 247-4, with 99.4 % 16S rRNA gene sequence similarity. Strain 213-9(3) shared the highest (93.9 %), (99.3 %) and concatenated and (97.5 %) sequence similarities to TMW 1.1424. Strain 30-1(2) had the highest (82.4 %), (95.5 %) and concatenated and (91.2 %) sequence similarities to 247-4. The phylogenetic relationships based on concatenated and sequences and whole genome sequences were identical to those based on 16S rRNA gene sequences. Strain 213-9(3) exhibited the highest average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values (92.7 and 48.8 %, respectively) to DSM 22467. Strain 30-1(2) had the highest ANI (84.4 %) and dDDH (32.8 %) values with 247-4. Acid production from -galactose, -glucose, -mannose, -acetyl--glucosaminidase, arbutin, salicin, cellobiose, maltose, gentiobiose, -tagatose and gluconate, hydrolysis of aesculin, and activity of cystine arylamidase could differentiate strain 213-9(3) from DSM 22467. Acid production from -arabinose, -ribose, -xylose and -galactose, and activity of alkaline phosphatase, esterase (C4), -mannosidase and -fucosidase could differentiate strain 30-1(2) from 247-4. Based upon the data obtained in the present study, two novel species, sp. nov. and sp. nov., are proposed and the type strains are 213-9(3) (=CCM 9241=CCTCC AB 2022115=JCM 35554) and 30-1(2) (=CCM 9240=CCTCC AB 2022114=JCM 35553), respectively.

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Keyword(s): lactic acid bacteria , Lapidilactobacillus , Levilactobacillus and pickle
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award no. 31471594)
    • Principle Award Recipient: Tao GuChun
© 2022 The Authors
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2022-12-20
2024-04-25
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References

  1. 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]
     [Google Scholar]
  2. Ehrmann MA, Preissler P, Danne M, Vogel RF. Lactobacillus paucivorans sp. nov., isolated from a brewery environment. Int J Syst Evol Microbiol 2010; 60:2353–2357 [View Article]
     [Google Scholar]
  3. Long GY, Gu CT. Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019; 69:2340–2353 [View Article]
     [Google Scholar]
  4. Valcheva R, Korakli M, Onno B, Prévost H, Ivanova I et al. Lactobacillus hammesii sp. nov., isolated from French sourdough. Int J Syst Evol Microbiol 2005; 55:763–767 [View Article] [PubMed]
     [Google Scholar]
  5. Hiraga K, Ueno Y, Sukontasing S, Tanasupawat S, Oda K. Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle. Int J Syst Evol Microbiol 2008; 58:1625–1629 [View Article] [PubMed]
     [Google Scholar]
  6. Zhang Z, Wang Y, Hou Q, Zhao H, Li W et al. Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium. Int J Syst Evol Microbiol 2020; 70:2580–2587 [View Article] [PubMed]
     [Google Scholar]
  7. Liu DD, Li YQ, Zhang LP, Ding W, Tian WL et al. Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., isolated from traditional Chinese pickle and the gut of honeybee (Apis mellifera). Int J Syst Evol Microbiol 2021; 71:004898
     [Google Scholar]
  8. Koob J, Jacob F, Wenning M, Hutzler M. Lactobacillus cerevisiae sp. nov., isolated from a spoiled brewery sample. Int J Syst Evol Microbiol 2017; 67:3452–3457 [View Article] [PubMed]
     [Google Scholar]
  9. Bui TPN, Kim YJ, In JG, Yang DC. Lactobacillus koreensis sp. nov., isolated from the traditional Korean food kimchi. Int J Syst Evol Microbiol 2011; 61:772–776 [View Article] [PubMed]
     [Google Scholar]
  10. Yi E-J, Yang J-E, Lee JM, Park Y, Park S-Y et al. Lactobacillus yonginensis sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi. Int J Syst Evol Microbiol 2013; 63:3274–3279 [View Article] [PubMed]
     [Google Scholar]
  11. Vancanneyt M, Neysens P, De Wachter M, Engelbeen K, Snauwaert C et al. Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov., from wheat sourdoughs. Int J Syst Evol Microbiol 2005; 55:615–620 [View Article] [PubMed]
     [Google Scholar]
  12. Long GY, Wei YX, Tu W, Gu CT. Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 2020; 70:2467–2484
     [Google Scholar]
  13. Guu J-R, Wang L-T, Hamada M, Wang C, Lin R-W et al. Lactobacillus bambusae sp. nov., isolated from traditional fermented ma bamboo shoots in Taiwan. Int J Syst Evol Microbiol 2018; 68:2424–2430 [View Article] [PubMed]
     [Google Scholar]
  14. Scheirlinck I, Van der Meulen R, Van Schoor A, Cleenwerck I, Huys G et al. Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough. Int J Syst Evol Microbiol 2007; 57:223–227 [View Article] [PubMed]
     [Google Scholar]
  15. Meroth CB, Hammes WP, Hertel C. Characterisation of the microbiota of rice sourdoughs and description of Lactobacillus spicheri sp. nov. Syst Appl Microbiol 2004; 27:151–159 [View Article] [PubMed]
     [Google Scholar]
  16. Liou J-S, Huang C-H, Wang C-L, Lee A-Y, Mori K et al. Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Int J Syst Evol Microbiol 2019; 69:1484–1489 [View Article] [PubMed]
     [Google Scholar]
  17. Lin S-T, Wang L-T, Wang H-M, Tamura T, Mori K et al. Lactobacillus suantsaicola sp. nov. and Lactobacillus suantsaiihabitans sp. nov., isolated from suan-tsai, a traditional fermented mustard green product of Taiwan. Int J Syst Evol Microbiol 2020; 70:2972–2980 [View Article] [PubMed]
     [Google Scholar]
  18. 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
     [Google Scholar]
  19. Tong H, Dong X. Lactobacillus concavus sp. nov., isolated from the walls of a distilled spirit fermenting cellar in China. Int J Syst Evol Microbiol 2005; 55:2199–2202 [View Article] [PubMed]
     [Google Scholar]
  20. Miyamoto M, Seto Y, Hao DH, Teshima T, Sun YB et al. Lactobacillus harbinensis sp. nov., consisted of strains isolated from traditional fermented vegetables “Suan cai” in Harbin, Northeastern China and Lactobacillus perolens DSM 12745. Syst Appl Microbiol 2005; 28:688–694 [View Article] [PubMed]
     [Google Scholar]
  21. Li TT, Liu DD, Fu ML, Gu CT. Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera). Int J Syst Evol Microbiol 2020; 70:3123–3133
     [Google Scholar]
  22. Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2013; 63:4094–4099 [View Article] [PubMed]
     [Google Scholar]
  23. An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043–2048 [View Article] [PubMed]
     [Google Scholar]
  24. Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P et al. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 2005; 151:2141–2150 [View Article]
     [Google Scholar]
  25. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  26. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 1989; 29:170–179 [View Article] [PubMed]
     [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  28. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  29. 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] [PubMed]
     [Google Scholar]
  30. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007; 57:2777–2789 [View Article] [PubMed]
     [Google Scholar]
  31. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. 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] [PubMed]
     [Google Scholar]
  35. 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]
  36. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. Yoon S-H, Ha S-M, 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]
  39. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  40. 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.
  41. Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics 2016; 17:356 [View Article] [PubMed]
     [Google Scholar]
  42. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
     [Google Scholar]
  43. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article] [PubMed]
     [Google Scholar]
  44. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  45. Tak EJ, Kim HS, Lee J-Y, Kang W, Hyun D-W et al. Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula. Int J Syst Evol Microbiol 2017; 67:3398–3402 [View Article] [PubMed]
     [Google Scholar]
  46. Sasser M. Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 1990
     [Google Scholar]
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Levilactobacillus humaensis sp. nov. and Lapidilactobacillus luobeiensis sp. nov., isolated from traditional Chinese pickle
Int J Syst Evol Microbiol 72, 005661 (2023); https://doi.org/10.1099/ijsem.0.005661
/content/journal/ijsem/10.1099/ijsem.0.005661
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