Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 4

Comparative genomic analysis of the genus and taxonomic study of sp. nov., isolated from Chinese rice wine starter No Access

Abstract

In this study, three lactic acid bacteria, namely, HBUAS51963, HBUAS51964 and HBUAS51965, were isolated from Chinese rice wine starter sampled in Fangxian County, PR China. All were non-motile, non-spore-forming and Gram-positive spherical cells. Their taxonomic status was characterized using a polyphasic approach. Genome-based analysis revealed that all three strains were phylogenomically related to KCTC 3751 and ATCC 33313. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the three strains and the phylogenetically related type strains were less than 54.8 and 93.8 %, respectively, and thus, they were below the thresholds of dDDH and ANI for species definition. The genomic DNA G+C content was 38.6 mol %. The predominant fatty acid methyl esters (>10 %) were C, C cyc11 and summed feature 10 (C cyc11 and/or ECL 17.834). The polar lipids in the cells of strain HBUAS51963 were mainly phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids, phospholipids and lipids. Finally, the three strains were capable of producing -lactic acid (4.29 g l) and various organic acids such as tartaric, acetic, lactic and succinic acids. Overall, the results of genotypic, phenotypic and genomic analyses suggest that the three strains represent a new species of the genus , for which the name sp. nov. is proposed. The type strain is HBUAS51963 (=GDMCC 1.3506= JCM 35803).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , rice wine starter , taxonomy and Weissella
Funding
This study was supported by the:
  • Hubei University of Arts and Science Cultivation Fund for Teachers' Scientific Research Ability: Technological Innovation Team (Award 2020kypytd009)
    • Principal Award Recipient: ZhuangGuo
  • Hubei Provincial Natural Science Foundation Joint Fund for Innovation and Development Project (Award 2022CFD008)
    • Principal Award Recipient: ZhuangGuo
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005870
2023-04-27
2025-12-15

Metrics

Loading full text...

Full text loading...

References

  1. Collins MD, Samelis J, Metaxopoulos J, Wallbanks S. 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 1993; 75:595–603 [View Article] [PubMed]
     [Google Scholar]
  2. Praet J, Meeus I, Cnockaert M, Houf K, Smagghe G et al. Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus bombicola sp. nov., and Weissella bombi sp. nov. Antonie van Leeuwenhoek 2015; 107:1337–1349 [View Article] [PubMed]
     [Google Scholar]
  3. Lee J-S, Lee KC, Ahn J-S, Mheen T-I, Pyun Y-R et al. Weissella koreensis sp. nov., isolated from Kimchi. Int J Syst Evol Microbiol 2002; 52:1257–1261 [View Article] [PubMed]
     [Google Scholar]
  4. Tanasupawat S, Shida O, Okada S, Komagata K. Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand. Int J Syst Evol Microbiol 2000; 50:1479–1485 [View Article] [PubMed]
     [Google Scholar]
  5. Li YQ, Tian WL, Gu CT. Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt. Int J Syst Evol Microbiol 2020; 70:2485–2492 [View Article] [PubMed]
     [Google Scholar]
  6. Magnusson J, Jonsson H, Schnürer J, Roos S. Weissella soli sp. nov., a lactic acid bacterium isolated from soil. Int J Syst Evol Microbiol 2002; 52:831–834 [View Article] [PubMed]
     [Google Scholar]
  7. Bello S, Rudra B, Gupta RS. 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 2022; 72:005284 [View Article]
     [Google Scholar]
  8. Zheng X-W, Tabrizi MR, Nout MJR, Han B-Z. Daqu- a traditional Chinese liquor fermentation starter. J I Brewing 2011; 117:82–90 [View Article]
     [Google Scholar]
  9. Yang Y, Hu W, Xia Y, Mu Z, Tao L et al. Flavor formation in Chinese rice wine (Huangjiu): impacts of the flavor-active microorganisms, raw materials, and fermentation technology. Front Microbiol 2020; 11:580247 [View Article] [PubMed]
     [Google Scholar]
  10. Chen L, Ren L, Li D, Ma X. Analysis of microbiomes in three traditional starters and volatile components of the Chinese rice wines. Food Sci Biotechnol 2021; 30:87–96 [View Article] [PubMed]
     [Google Scholar]
  11. Cai H, Zhang T, Zhang Q, Luo J, Cai C et al. Microbial diversity and chemical analysis of the starters used in traditional Chinese sweet rice wine. Food Microbiol 2018; 73:319–326 [View Article] [PubMed]
     [Google Scholar]
  12. Chen G-M, Huang Z-R, Wu L, Wu Q, Guo W-L et al. Microbial diversity and flavor of Chinese rice wine (Huangjiu): an overview of current research and future prospects. Curr Opin Food Sci 2021; 42:37–50 [View Article]
     [Google Scholar]
  13. Yang Y, Xia Y, Wang G, Yu J, Ai L. Effect of mixed yeast starter on volatile flavor compounds in Chinese rice wine during different brewing stages. LWT 2017; 78:373–381 [View Article]
     [Google Scholar]
  14. 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]
  15. Nero LA, Beloti V, De Aguiar Ferreira Barros M, Ortolani MBT, Tamanini R et al. Comparison of Petrifilm aerobic count plates and de Man–Rogosa–Sharpe agar for enumeration of lactic acid bacteria. J Rapid Methods Auto Microbiol 2006; 14:249–257 [View Article]
     [Google Scholar]
  16. Sakamoto M, Takeuchi Y, Umeda M, Ishikawa I, Benno Y. Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J Med Microbiol 2003; 52:79–89 [View Article] [PubMed]
     [Google Scholar]
  17. Marchuk D, Drumm M, Saulino A, Collins FS. Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res 1991; 19:1154 [View Article] [PubMed]
     [Google Scholar]
  18. 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] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  22. Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 2014; 15:1–9 [View Article] [PubMed]
     [Google Scholar]
  23. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
     [Google Scholar]
  24. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  25. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  26. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  27. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [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; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  29. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:1–10 [View Article] [PubMed]
     [Google Scholar]
  30. Galindo LJ, López-García P, Torruella G, Karpov S, Moreira D. Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota. Nat Commun 2021; 12:4973 [View Article] [PubMed]
     [Google Scholar]
  31. 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] [PubMed]
     [Google Scholar]
  32. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–7 [View Article] [PubMed]
     [Google Scholar]
  33. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  34. Gerhardt P, Murray R, Costilow R, Nester EW, Wood WA et al. Manual of methods for general bacteriology 1981
     [Google Scholar]
  35. Handley PS, Carter PL, Wyatt JE, Hesketh LM. Surface structures (peritrichous fibrils and tufts of fibrils) found on Streptococcus sanguis strains may be related to their ability to coaggregate with other oral genera. Infect Immun 1985; 47:217–227 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Da X, Jiang F, Chang X, Ren L, Qiu X et al. Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica. Int J Syst Evol Microbiol 2015; 65:3841–3846 [View Article] [PubMed]
     [Google Scholar]
  38. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  39. 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]
  40. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  41. 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]
  42. 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]
  43. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Kwak M-J, Choi S-B, Kim B-Y, Chun J. Genome-based reclassification of Weissella jogaejeotgali as a later heterotypic synonym of Weissella thailandensis. Int J Syst Evol Microbiol 2019; 69:3672–3675 [View Article] [PubMed]
     [Google Scholar]
  46. Kawaguchi H, Vertès AA, Okino S, Inui M, Yukawa H. Engineering of a xylose metabolic pathway in Corynebacterium glutamicum. Appl Environ Microbiol 2006; 72:3418–3428 [View Article] [PubMed]
     [Google Scholar]
  47. Munné-Bosch S, Falk J. New insights into the function of tocopherols in plants. Planta 2004; 218:323–326 [View Article] [PubMed]
     [Google Scholar]
  48. Barja MV, Ezquerro M, Beretta S, Diretto G, Florez-Sarasa I et al. Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato. New Phytol 2021; 231:255–272 [View Article] [PubMed]
     [Google Scholar]
  49. Kallscheuer N, Moreira C, Airs R, Llewellyn CA, Wiegand S et al. Pink- and orange-pigmented Planctomycetes produce saproxanthin-type carotenoids including a rare C45 carotenoid. Environ Microbiol Rep 2019; 11:741–748 [View Article] [PubMed]
     [Google Scholar]
  50. Zhang Y, Geary T, Simpson BK. Genetically modified food enzymes: a review. Curr Opin Food Sci 2019; 25:14–18 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005870
Loading
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 (2023); https://doi.org/10.1099/ijsem.0.005870
/content/journal/ijsem/10.1099/ijsem.0.005870
/content/journal/ijsem/10.1099/ijsem.0.005870
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