1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 4

sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., isolated from Chinese traditional pickle and yogurt Free

Abstract

Fourteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and yogurt. The strains were characterized using a polyphasic taxonomic approach, including 16S rRNA gene sequence analysis, gene sequence analysis, gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, determination of average nucleotide identity (ANI), DNA–DNA hybridization (DDH) and an analysis of phenotypic features. The data demonstrated that the 14 strains represented ten novel species belonging to the genus , strains 73-4, 247-3, 143-4(a), 33-1, 143-6, 247-4, 17-4, 143-1, 735-2 and M1530-1 were designated as the type strains. Strains 73-4 and 247-3 were phylogenetically related to the type strains of and , having 97.0–98.9 % 16S rRNA gene sequence similarities, 83.9–87.2 %  gene sequence similarities and 86.8–93.3 %  gene sequence similarities. Strains 143-4(a) and 33-1 were phylogenetically related to the type strains of , and , having 93.6–96.5 % 16S rRNA gene sequence similarities, 73.9–77.2 %  gene sequence similarities and 76.1–77.6 %  gene sequence similarities. Strains 143-6, 247-4, 17-4 and 143-1 were phylogenetically related to the type strains of , and , exhibiting 95.5–99.9 % 16S rRNA gene sequence similarities, 76.5–83.1 %  gene sequence similarities and 83.6–98.3 %  gene sequence similarities. Strain 735-2 was phylogenetically related to the type strains of , and , having 98.2–99.1 % 16S rRNA gene sequence similarities, 82.8–84.1 %  gene sequence similarities and 93.0–93.9 %  gene sequence similarities. Strain M1530-1 was phylogenetically related to the type strains of and , having 99.5 and 99.0 % 16S rRNA gene sequence similarities, 90.3 and 81.7 %  gene sequence similarities and 97.7 and 91.1 %  gene sequence similarities. The ANI and DDH values between strains 73-4, 247-3, 143-4(a), 33-1, 143-6, 247-4, 17-4, 143-1, 735-2, M1530-1 and type strains of phylogenetically related species were less than 86.8 % and 33.9 % respectively, confirming that they represent ten novel species within the genus . Based upon the data of polyphasic characterization obtained in the present study, ten novel species, sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., are proposed and the type strains are 73-4 (=NCIMB 15177=CCM 8912=CCTCC AB 2018407), 247-3 (=NCIMB 15176=JCM 33275), 143-4(a) (=NCIMB 15173=CCM 8948=JCM 33273=CCTCC AB 2018390), 33-1 (=NCIMB 15169=CCM 8947=JCM 33272=CCTCC AB 2018405), 143-6 (=NCIMB 15162=CCM 8951=JCM 33274=CCTCC AB 2018411), 247-4 (=NCIMB 15155=CCM 8897=LMG 31059=CCTCC AB 2018410), 17-4 (=NCIMB 15161=CCM 8946=JCM 33271=CCTCC AB 2018406), 143-1 (=NCIMB 15157=CCM 8937=CCTCC AB 2018409), 735-2 (=NCIMB 15190=CCM 8925=LMG 31186) and M1530-1 (=NCIMB 15150=CCM 8893=LMG 31046=CCTCC AB 2018402), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): lactic acid bacteria , Lactobacillus , novel species , pickle and yogurt
Funding
This study was supported by the:
  • the National Natural Science Foundation of China (Award no. 31471594)
    • Principle Award Recipient: Chun Tao Gu
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004060
2020-02-26
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2467.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004060&mimeType=html&fmt=ahah

References

  1. De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W. (editors) Taxonomic outline of the phylum Firmicutes . Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp 15–17
     [Google Scholar]
  2. Hammes WP, Hertel C. Genus Lactobacillus Beijerink, 1901. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. (editors) Bergey’s Manual of Systematic Bacteriology 3, 2nd ed. Berlin: Springer; 2009 pp 465–.510
     [Google Scholar]
  3. 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]
     [Google Scholar]
  4. Gu CT, Wang F, Li CY, Liu F, Huo GC. Lactobacillus xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2012; 62:860–863 [View Article]
     [Google Scholar]
  5. 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]
     [Google Scholar]
  6. Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. Int J Syst Evol Microbiol 2013; 63:4698–4706 [View Article]
     [Google Scholar]
  7. Zhao W, Gu CT. Lactobacillus hulanensis sp. nov., isolated from suancai, a traditional Chinese pickle. Int J Syst Evol Microbiol 2019; 69:2147–2152 [View Article]
     [Google Scholar]
  8. 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]
  9. Fu ML, Gu CT. Lactobacillus huachuanensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019; 69:2807–2814 [View Article]
     [Google Scholar]
  10. 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]
  11. Liu DD, Gu CT. Lactobacillus pingfangensis sp. nov., Lactobacillus daoliensis sp. nov., Lactobacillus nangangensis sp. nov., Lactobacillus daowaiensis sp. nov., Lactobacillus dongliensis sp. nov., Lactobacillus songbeiensis sp. nov. and Lactobacillus kaifaensis sp. nov., isolated from traditional Chinese pickle. Int J Syst Evol Microbiol 2019; 69:3237–3247 [View Article]
     [Google Scholar]
  12. Li CY, Tian F, Zhao YD, Gu CT. Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2014; 64:1012–1017 [View Article]
     [Google Scholar]
  13. Li YQ, Gu CT. Enterococcus pingfangensis sp. nov., Enterococcus dongliensis sp. nov., Enterococcus hulanensis sp. nov., Enterococcus nangangensis sp. nov. and Enterococcus songbeiensis sp. nov., isolated from Chinese traditional pickle juice. Int J Syst Evol Microbiol 2019; 69:3191–3201 [View Article]
     [Google Scholar]
  14. 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]
     [Google Scholar]
  15. 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]
  16. 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]
     [Google Scholar]
  17. 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]
  18. 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]
     [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]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. 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]
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. 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]
     [Google Scholar]
  24. 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]
  25. 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]
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. 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 Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  30. 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]
  31. Mattarelli P, Holzapfel W, Franz CM, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article]
     [Google Scholar]
  32. Krieg NR, Padgett PJ. Phenotypic and physiological characterization methods. Methods Microbiol 2011; 38:15–60
     [Google Scholar]
  33. Miyashita M, Yukphan P, Chaipitakchonlatarn W, Malimas T, Sugimoto M et al. Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods. Int J Syst Evol Microbiol 2015; 65:2485–2490 [View Article]
     [Google Scholar]
  34. 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]
  35. 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]
     [Google Scholar]
  36. Akopyanz N, Bukanov NO, Westblom TU, Kresovich S, Berg DE. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res 1992; 20:5137–5142 [View Article]
     [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101.. Newark, DE, USA: Microbial ID Inc; 1990
     [Google Scholar]
  38. Tanasupawat S, Pakdeeto A, Thawai C, Yukphan P, Okada S. Identification of lactic acid bacteria from fermented tea leaves (miang) in Thailand and proposals of Lactobacillus thailandensis sp. nov., Lactobacillus camelliae sp. nov., and Pediococcus siamensis sp. nov. J Gen Appl Microbiol 2007; 53:7–15 [View Article]
     [Google Scholar]
  39. Cai Y, Pang H, Kitahara M, Ohkuma M. Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus . Int J Syst Evol Microbiol 2012; 62:1140–1144 [View Article]
     [Google Scholar]
  40. Morlon-Guyot J, Guyot JP, Pot B, Jacobe de Haut I, Raimbault M. Lactobacillus manihotivorans sp. nov., a new starch-hydrolysing lactic acid bacterium isolated during cassava sour starch fermentation. Int J Syst Bacteriol 1998; 48 Pt 4:1101–1109 [View Article]
     [Google Scholar]
  41. Nguyen DTL, Cnockaert M, Van Hoorde K, De Brandt E, Snauwaert I et al. Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua. Int J Syst Evol Microbiol 2013; 63:1754–1759 [View Article]
     [Google Scholar]
  42. Liu B, Dong X. Lactobacillus pantheris sp. nov., isolated from faeces of a jaguar. Int J Syst Evol Microbiol 2002; 52:1745–1748 [View Article]
     [Google Scholar]
  43. Weiss N, Schillinger U, Laternser M, Kandler O. Lactobacillus sharpeae sp. nov. and Lactobacillus agilis sp. nov., two new species of homofermentative, meso-diaminopimelic acid-containing lactobacilli isolated from sewage. Zbl Bakt Hyg I Abt Orig C 1981; 2:242–253
     [Google Scholar]
  44. Collins MD, Phillips BA, Zanoni P. Deoxyribonucleic acid homology studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and Lactobacillus rhamnosus sp. nov., comb. nov. Int J Syst Bacteriol 1989; 39:105–108 [View Article]
     [Google Scholar]
  45. Dicks LM, Du Plessis EM, Dellaglio F, Lauer E. Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei . Int J Syst Bacteriol 1996; 46:337–340 [View Article]
     [Google Scholar]
  46. Mills CK, Lessel EF. Lactobacterium zeae Kuznetsov, a later subjective synonym of Lactobacillus casei (Orla-Jensen) Hansen and Lessel. Int J Syst Bacteriol 1973; 23:430–432 [View Article]
     [Google Scholar]
  47. Huang C-H, Liou J-S, Lee A-Y, Tseng M, Miyashita M et al. Polyphasic characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: Description of L. chiayiensis sp. nov. Syst Appl Microbiol 2018; 41:270–278 [View Article]
     [Google Scholar]
  48. 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]
     [Google Scholar]
  49. Back W. Elevation of Pediococcus cerevisiae subsp. dextrinicus Coster and White to species status [Pediococcus dextrinicus (Coster and White) comb. nov.]. Int J Syst Bacteriol 1978; 28:523–527 [View Article]
     [Google Scholar]
  50. Kandler O, Weiss N. Genus Lactobacillus beijerinck 1901, 212AL . In Sneath PHA, Mair NS, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology 2 Baltimore: Williams & Wilkins; 1986 pp 1209–1234
     [Google Scholar]
  51. Chenoll E, Macián MC, Aznar R. Lactobacillus rennini sp. nov., isolated from rennin and associated with cheese spoilage. Int J Syst Evol Microbiol 2006; 56:449–452 [View Article]
     [Google Scholar]
  52. Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R et al. Description of Lactobacillus iwatensis sp. nov., isolated from orchardgrass (Dactylis glomerata L.) silage, and Lactobacillus backii sp. nov. Int J Syst Evol Microbiol 2013; 63:3854–3860 [View Article]
     [Google Scholar]
  53. 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 2019 14 Jun 2019 [View Article]
     [Google Scholar]
  54. 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]
     [Google Scholar]
  55. 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]
     [Google Scholar]
  56. Vancanneyt M, Naser SM, Engelbeen K, De Wachter M, Van der Meulen R et al. Reclassification of Lactobacillus brevis strains LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 2006; 56:1553–1557 [View Article]
     [Google Scholar]
  57. 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; 63:1140–1144 [View Article]
     [Google Scholar]
  58. Bui TPN, Kim Y-J, In J-G, Yang D-C. Lactobacillus koreensis sp. nov., isolated from the traditional Korean food kimchi. Int J Syst Evol Microbiol 2011; 61:772–776 [View Article]
     [Google Scholar]
  59. 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]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004060
Loading
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 70, 2467 (2020); https://doi.org/10.1099/ijsem.0.004060
/content/journal/ijsem/10.1099/ijsem.0.004060
/content/journal/ijsem/10.1099/ijsem.0.004060
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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