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Volume 72, Issue 5

subsp. subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product No Access

Abstract

Two lactic acid bacterial strains (IMAU80584 and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to . However, phylogenetic tree analyses of two housekeeping genes, (encoding RNA polymerase alpha subunit) and (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from DSM 19907, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584 and DSM 19907 were 93.1 and 52.8 %, respectively. Strains IMAU80584 and IMAU92037 are distinguished from DSM 19907 because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584 was 42.3 mol%. The major cellular fatty acids were C, C 9t and summed feature 5 (C ante and/or C 6 and/or C 9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584 and IMAU92037 could be considered as a novel subspecies in the species with the proposed name subsp. subsp. nov. The type strain is IMAU80584 (=GDMCC 1.2566=JCM 34647).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): lactic acid bacteria , Lentilactobacillus rapi subsp. dabitei subsp. nov. , naturally fermented dairy product and novel subspecies
Funding
This study was supported by the:
  • Inner Mongolia Autonomous Region Science and Technology Project (Award 2021GG0080)
    • Principle Award Recipient: NotApplicable
  • Major projects of Natural Science Foundation of Inner Mongolia Autonomous Region (Award 2019ZD06)
    • Principle Award Recipient: NotApplicable
  • National Natural Science Foundation of China (Award No. 31972095)
    • Principle Award Recipient: NotApplicable
© 2022 The Authors
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2022-05-06
2024-05-03
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References

  1. Watanabe K, Fujimoto J, Sasamoto M, Dugersuren J, Tumursuh T et al. Diversity of lactic acid bacteria and yeasts in Airag and Tarag, traditional fermented milk products of Mongolia. World J Microbiol Biotechnol 2007; 24:1313–1325 [View Article]
     [Google Scholar]
  2. Zhang H. Biodiversity of lactic acid bacteria in naturally fermented dairy products. Chin Bull Life Sci 2015; 27:837–846
     [Google Scholar]
  3. Sidorenko OD, Pastukh ON, Zhukova EV, Garaeva GV et al. Microbial community of natural starter of fermented dairy product. IOP Conf Ser: Earth Environ Sci 2021; 640:032003 [View Article]
     [Google Scholar]
  4. Lavefve L, Howard LR, Carbonero F. Berry polyphenols metabolism and impact on human gut microbiota and health. Food Funct 2020; 11:45–65 [View Article] [PubMed]
     [Google Scholar]
  5. Quigley L, O’Sullivan O, Stanton C, Beresford TP, Ross RP et al. The complex microbiota of raw milk. FEMS Microbiol Rev 2013; 37:664–698 [View Article] [PubMed]
     [Google Scholar]
  6. Beijerinck MW. Sur les ferments lactiques de l'industrie. Archiv Neerlandaises des Sciences Exactes et Naturelles 1901; 6:212–243
     [Google Scholar]
  7. Sun Z, Harris HMB, McCann A, Guo C, Argimón S et al. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 2015; 6:8322 [View Article] [PubMed]
     [Google Scholar]
  8. Zheng J, Wittouck S, Salvetti E, Franz CMAP, 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]
  9. Bao Q, Liu W, Yu J, Wang W, Qing M et al. Isolation and identification of cultivable lactic acid bacteria in traditional yak milk products of Gansu Province in China. J Gen Appl Microbiol 2012; 58:95–105 [View Article] [PubMed]
     [Google Scholar]
  10. Yu J, Wang HM, Zha MS, Qing YT, Bai N et al. Molecular identification and quantification of lactic acid bacteria in traditional fermented dairy foods of Russia. J Dairy Sci 2015; 98:5143–5154 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. Kim M, Oh H-S, Park S-C, Chun J et al. 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] [PubMed]
     [Google Scholar]
  15. Torriani S, Felis GE, Dellaglio F. Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl Environ Microbiol 2001; 67:3450–3454 [View Article]
     [Google Scholar]
  16. 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]
  17. 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] [PubMed]
     [Google Scholar]
  18. Seng P, Rolain J-M, Fournier PE, La Scola B, Drancourt M et al. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733–1754 [View Article] [PubMed]
     [Google Scholar]
  19. De Florio L, Riva E, Giona A, Dedej E, Fogolari M et al. MALDI-TOF MS identification and clustering applied to enterobacter species in nosocomial setting. Front Microbiol 2018; 9:8 [View Article] [PubMed]
     [Google Scholar]
  20. Li Y, Shan M, Zhu Z, Mao X, Yan M et al. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:11 [View Article] [PubMed]
     [Google Scholar]
  21. Hill V, Kuhnert P, Erb M, Machado RAR et al. Identification of Photorhabdus symbionts by MALDI-TOF MS. Microbiology 2020; 166:522–530 [View Article] [PubMed]
     [Google Scholar]
  22. Christensen H, Kuhnert P, Busse H-J, Frederiksen WC, Bisgaard M et al. Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae. Int J Syst Evol Microbiol 2007; 57:166–178 [View Article] [PubMed]
     [Google Scholar]
  23. Luo R, Liu B, Xie Y, Li Z, Huang W et al. Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2015; 4:1 [View Article] [PubMed]
     [Google Scholar]
  24. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  25. 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] [PubMed]
     [Google Scholar]
  26. Chen C, Chen H, Zhang Y, Thomas HR, Frank MH et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 2020; 13:1194–1202 [View Article] [PubMed]
     [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  28. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
     [Google Scholar]
  33. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article] [PubMed]
     [Google Scholar]
  34. Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M et al. Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage. Int J Syst Evol Microbiol 2017; 67:3639–3644 [View Article] [PubMed]
     [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  36. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
     [Google Scholar]
  37. Yao JK, Rastetter GM. Microanalysis of complex tissue lipids by high-performance thin-layer chromatography. Anal Biochem 1985; 150:111–116 [View Article] [PubMed]
     [Google Scholar]
  38. Schumann P. Peptidoglycan structure. In Rainey F, eds OA. eds Methods In Microbiology, Vol 38: Taxonomy Of Prokaryotes San Diego: Elsevier Academic Press Inc; 2011 pp 101–129
     [Google Scholar]
  39. Yoon M-H, Ten LN, Im W-T, Lee S-T. Cellulomonas chitinilytica sp nov., a chitinolytic bacterium isolated from cattle-farm compost. Int J Syst Evol Microbiol 2008; 58:1878–1884 [View Article] [PubMed]
     [Google Scholar]
  40. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  41. Wu X, Brooks BR. International Code of Nomenclature of Bacteria Bacteriological Code. FEMS Microbiol Lett 1992; 94:i [View Article]
     [Google Scholar]
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Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product
Int J Syst Evol Microbiol 72, 005359 (2022); https://doi.org/10.1099/ijsem.0.005359
/content/journal/ijsem/10.1099/ijsem.0.005359
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