Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi

  • Jae Kyeong Lee (Department of Life Science, Chung-Ang University) ;
  • Ju Hye Baek (Department of Life Science, Chung-Ang University) ;
  • Dong Min Han (Department of Life Science, Chung-Ang University) ;
  • Se Hee Lee (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • So Young Kim (Department of Agro-Food Resources, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Che Ok Jeon (Department of Life Science, Chung-Ang University)
  • Received : 2023.06.07
  • Accepted : 2023.07.18
  • Published : 2023.11.28
Download PDF
⟨ Previous Next ⟩

Abstract

A Gram-positive, non-motile, and non-spore-forming lactic acid bacterium, designated as BK2T, was isolated from kimchi, a Korean traditional fermented vegetable food, and the taxonomic characteristics of strain BK2T, along with strain LMG 11983, were analyzed. Both strains optimally grew at 30℃, pH 7.0, and 1.0% NaCl. Cells of both strains were heterofermentative and facultatively anaerobic rods, demonstrating negative reactions for catalase and oxidase. Major fatty acids (>10%) identified in both strains were C18:1 ω9c, C16:0, and summed feature 7 (comprising C19:1 ω6c and/or C19:1 ω7c). The genomic DNA G+C contents of both strains were 44.7 mol%. The 16S rRNA gene sequence similarity (99.9%), average nucleotide identity (ANI; 99.9%), and digital DNA-DNA hybridization (dDDH; 99.7%) value between strains BK2T and LMG 11983 indicated that they are different strains of the same species. Strain BK2T was most closely related to Weissella confusa JCM 1093T and Weissella cibaria LMG 17699T, with 100% and 99.4% 16S rRNA gene sequence similarities, respectively. However, based on the ANI and dDDH values (92.3% and 48.1% with W. confusa, and 78.4% and 23.5% with W. cibaria), it was evident that strain BK2T represents a distinct species separate from W. confusa and W. cibaria. Based on phylogenetic, phenotypic, and chemotaxonomic features, strains BK2T and LMG 11983 represent a novel species of the genus Weissella, for which the name Weissella fermenti sp. nov. is proposed. The type of strain is BK2T (=KACC 22833T=JCM 35750T).

Keywords

Acknowledgement

This work was supported by the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01710102), RDA; and the National Institute of Biological Resources (NIBR No. 2022-02-001), Republic of Korea.

References

  1. Collins MD, Samelis J, Metaxopoulos J, Wallbanks S. 1993. Taxonomic studies on some leuconostoc-like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species. J. Appl. Bacteriol. 75: 595-603. https://doi.org/10.1111/j.1365-2672.1993.tb01600.x
  2. Bello S, Rudra B, Gupta RS. 2022. Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov. Int. J. Syst. Evol. Microbiol. 72: 005284.
  3. Lee JS, Lee KC, Ahn JS, Mheen TI, Pyun YR, Park YH. 2002. Weissella koreensis sp. nov., isolated from kimchi. Int. J. Syst. Evol. Microbiol. 52: 1257-1261. https://doi.org/10.1099/00207713-52-4-1257
  4. Li YQ, Tian WL, Gu CT. 2020. Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt. Int. J. Syst. Evol. Microbiol. 70: 2485-2492. https://doi.org/10.1099/ijsem.0.004062
  5. Tanasupawat S, Shida O, Okada S, Komagata K. 2000. Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand. Int. J. Syst. Evol. Microbiol. 50: 1479-1485. https://doi.org/10.1099/00207713-50-4-1479
  6. Tohno M, Kitahara M, Inoue H, Uegaki R, Irisawa T, Ohkuma M, et al. 2013. Weissella oryzae sp. nov., isolated from fermented rice grains. Int. J. Syst. Evol. Microbiol. 63: 1417-1420. https://doi.org/10.1099/ijs.0.043612-0
  7. Xiang F, Dong Y, Cai W, Zhao H, Liu H, Shan C, et al. 2023. Comparative genomic analysis of the genus Weissella and taxonomic study of Weissella fangxianensis sp. nov., isolated from Chinese rice wine starter. Int. J. Syst. Evol. Microbiol. 73: 005870.
  8. Holzapfel W, Kandler O. 1969. Taxonomy of the species Lactobacillus Beijerinck. VI. Lactobacillus coprophilus subsp. confusus nov. subsp., a new variety of the subspecies Betabacterium. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. 123: 657-666.
  9. Fusco V, Quero GM, Cho GS, Kabisch J, Meske D, Neve H, et al. 2015. The genus Weissella: taxonomy, ecology and biotechnological potential. Front Microbiol. 6: 155.
  10. Hyun DW, Lee JY, Sung H, Kim PS, Jeong YS, Lee JY, et al. 2021. Brevilactibacter coleopterorum sp. nov., isolated from the intestine of the dark diving beetle Hydrophilus acuminatus, and Weissella coleopterorum sp. nov., isolated from the intestine of the diving beetle Cybister lewisianus. Int. J. Syst. Evol. Microbiol. 71: 004779.
  11. Oh SJ, Shin NR, Hyun DW, Kim PS, Kim JY, Kim MS, et al. 2013. Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana). Int. J. Syst. Evol. Microbiol. 63: 2951-2956. https://doi.org/10.1099/ijs.0.047548-0
  12. Magnusson J, Jonsson H, Schnurer J, Roos S. 2002. Weissella soli sp. nov., a lactic acid bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 52: 831-834. https://doi.org/10.1099/00207713-52-3-831
  13. Heo J, Hamada M, Cho H, Weon HY, Kim JS, Hong SB, et al. 2019. Weissella cryptocerci sp. nov., isolated from gut of the insect Cryptocercus kyebangensis. Int. J. Syst. Evol. Microbiol. 69: 2801-2806. https://doi.org/10.1099/ijsem.0.003564
  14. Lin ST, Wang LT, Wu YC, Guu JRJ, Tamura T, Mori K, et al. 2020. Weissella muntiaci sp. nov., isolated from faeces of Formosan barking deer (Muntiacus reevesi). Int. J. Syst. Evol. Microbiol. 70: 1578-1584. https://doi.org/10.1099/ijsem.0.003937
  15. Vela AI, Fernandez A, Bernaldo de Quiros Y, Herraez P, Dominguez L, Fernandez-Garayzabal JF. 2011. Weissella ceti sp. nov., isolated from beaked whales (Mesoplodon bidens). Int. J. Syst. Evol. Microbiol. 61: 2758-2762. https://doi.org/10.1099/ijs.0.028522-0
  16. Rainey F, Kampfer P, Trujillo M, Chun J, DeVos P, Hedlund B, et al. 2015. In Whitman WB (ed.). Bergey's Manual of Systematics of Archaea and Bacteria, Vol. 410. Wiley, Hoboken, NJ.
  17. Lim SK, Kwon MS, Lee J, Oh YJ, Jang JY, Lee JH, et al. 2017. Weissella cibaria WIKIM28 ameliorates atopic dermatitis-like skin lesions by inducing tolerogenic dendritic cells and regulatory T cells in BALB/c mice. Sci. Rep. 7: 40040.
  18. Yu HS, Lee NK, Choi AJ, Choe JS, Bae CH, Paik HD. 2019. Anti-inflammatory potential of probiotic strain Weissella cibaria JW15 isolated from kimchi through regulation of NF-κB and MAPKs pathways in LPS-induced RAW 264.7 cells. J. Microbiol. Biotechnol. 29: 1022-1032. https://doi.org/10.4014/jmb.1903.03014
  19. Park HE, Kang KW, Kim BS, Lee SM, Lee WK. 2017. Immunomodulatory potential of Weissella cibaria in aged C57BL/6J mice. J. Microbiol. Biotechnol. 27: 2094-2103. https://doi.org/10.4014/jmb.1708.08016
  20. Park JA, Tirupathi Pichiah PB, Yu JJ, Oh SH, Daily JW, Cha YS. 2012. Anti-obesity effect of kimchi fermented with Weissella koreensis OK1-6 as starter in high-fat diet-induced obese C57BL/6J mice. J. Appl. Microbiol. 113: 1507-1516. https://doi.org/10.1111/jam.12017
  21. Jeong SE, Chun BH, Kim KH, Park D, Roh SW, Lee SH, et al. 2018. Genomic and metatranscriptomic analyses of Weissella koreensis reveal its metabolic and fermentative features during kimchi fermentation. Food Microbiol. 76: 1-10. https://doi.org/10.1016/j.fm.2018.04.003
  22. Baek JH, Kim KH, Han DM, Lee SH, Jeon CO. 2023. Effects of glutinous rice paste and fish sauce on kimchi fermentation. LWT 173: 114253.
  23. Khan SA, Kim HM, Baek JH, Jung HS, Jeon CO. 2021. Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., isolated from soil. J. Microbiol. Biotechnol. 31: 1210-1217. https://doi.org/10.4014/jmb.2105.05023
  24. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617. https://doi.org/10.1099/ijsem.0.001755
  25. Nawrocki EP, Eddy SR. 2007. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol. 3: e56.
  26. Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  27. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37: 540-546. https://doi.org/10.1038/s41587-019-0072-8
  28. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9: e112963.
  29. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25: 1043-1055. https://doi.org/10.1101/gr.186072.114
  30. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44: 6614-6624. https://doi.org/10.1093/nar/gkw569
  31. Kim J, Na SI, Kim D, Chun J. 2021. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J. Microbiol. 59: 609-615. https://doi.org/10.1007/s12275-021-1231-4
  32. Lee I, Kim YO, Park SC, Chun J. 2016. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66: 1100-1103. https://doi.org/10.1099/ijsem.0.000760
  33. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
  34. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. https://doi.org/10.1093/bioinformatics/btq461
  35. Gomori G. 1955. Preparation of buffers for use in enzyme studies. Methods Enzymol. 1: 138-146. https://doi.org/10.1016/0076-6879(55)01020-3
  36. Lanyi B. 1987. 1 Classical and rapid identification methods for medically important bacteria. Methods Microbiol. 19: 1-67. https://doi.org/10.1016/S0580-9517(08)70407-0
  37. Smibert RM, Krieg NR. 1994. Phenotypic characterization, pp. 607-654. In Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds.), Methods for General and Molecular Bacteriology, American Society for Microbiology. Washington D.C.
  38. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. 1977. Polar lipid composition in the classification of Nocardia and related bacteria. Int. J. Syst. Evol. Microbiol. 27: 104-117. https://doi.org/10.1099/00207713-27-2-104
  39. Kim M, Oh HS, Park SC, Chun J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64: 346-351. https://doi.org/10.1099/ijs.0.059774-0
  40. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712. https://doi.org/10.1126/science.1138140
  41. Choi EJ, Jin HM, Lee SH, Math RK, Madsen EL, Jeon CO. 2013. Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59. Appl. Environ. Microbiol. 79: 663-671. https://doi.org/10.1128/AEM.02809-12
  42. Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106