Skip to content
1887

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

Volume 75, Issue 1

sp. nov. isolated from flowers of winter savoury L. Open Access

Abstract

A novel strain of the genus , named He02, was isolated from flowers of L. in a survey for lactic acid bacteria associated with wild and cultivated plants in the metropolitan area of Valencia, Spain. Partial 16S rRNA gene sequencing revealed a similarity of 99% to DSM 23037=Ryu1-2. Strain He02 cells are Gram-stain-positive, catalase-negative non-motile rods, usually occurring in pairs. Cells show a pale yellow pigmentation when pelleted. As , strain He02 utilized a narrow range of carbohydrates, namely, glucose and fructose, homofermentatively. However, genome sequencing and estimation of average nucleotide identity (ANI) revealed an ANI value of 87.44 with DSM 23037, the only strain sequenced to date. A value of 30.5% for digital DNA–DNA hybridization was estimated with the Type Strain Genome Server tool when He02 was compared with strain DSM 23037. These results indicate that strain He02 constitutes a novel species, for which the name sp. nov. with He02 (=CECT 31001=DSM 117324=CCM 9395) as type strain is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): flower , Holzapfeliella , Satureja montana and Valencia
Funding
This study was supported by the:
  • Agencia Estatal de Investigación (Award PID2020-11960RB-I00)
    • Principal Award Recipient: JoséMaría Landete
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006654
2025-01-22
2025-12-05

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/1/ijsem006654.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006654&mimeType=html&fmt=ahah

References

  1. Orozco-Mosqueda M del C, Rocha-Granados M del C, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res 2018; 208:25–31 [View Article]
     [Google Scholar]
  2. Yu AO, Leveau JHJ, Marco ML. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. Environ Microbiol Rep 2020; 12:16–29 [View Article] [PubMed]
     [Google Scholar]
  3. Endo A, Maeno S, Tanizawa Y, Kneifel W, Arita M et al. Fructophilic lactic acid bacteria, a unique group of fructose-fermenting microbes. Appl Environ Microbiol 2018; 84:e01290–01218 [View Article] [PubMed]
     [Google Scholar]
  4. Konno N, Maeno S, Tanizawa Y, Arita M, Endo A et al. Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments. Commun Biol 2024; 7:902 [View Article] [PubMed]
     [Google Scholar]
  5. Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y et al. Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers. Int J Syst Evol Microbiol 2011; 61:1356–1359 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
     [Google Scholar]
  7. Deshmukh UB, Oren A. Proposal of Holzapfeliella gen. nov. and Litorivicinus gen. nov. as replacement names for the illegitimate prokaryotic generic names Holzapfelia Zheng et al. 2020 and Litoricola Kim et al. 2007, respectively. Int J Syst Evol Microbiol 2023; 73:005688 [View Article]
     [Google Scholar]
  8. Endo A, Futagawa-Endo Y, Dicks LMT. Isolation and characterization of fructophilic lactic acid bacteria from fructose-rich niches. Syst Appl Microbiol 2009; 32:593–600 [View Article] [PubMed]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–175
     [Google Scholar]
  10. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Minh BQ, Nguyen MAT, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 2013; 30:1188–1195 [View Article] [PubMed]
     [Google Scholar]
  13. Parente E, Zotta T, Giavalisco M, Ricciardi A. Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 2023; 391–393:110124 [View Article] [PubMed]
     [Google Scholar]
  14. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
     [Google Scholar]
  15. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  16. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  17. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Manni M, Berkeley MR, Seppey M, Zdobnov EM. BUSCO: assessing genomic data quality and beyond. Curr Protoc 2021; 1:e323 [View Article] [PubMed]
     [Google Scholar]
  20. Community TG. The galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Res 2024
     [Google Scholar]
  21. Tian R, Imanian B. VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution. Microbiome 2023; 11:247 [View Article] [PubMed]
     [Google Scholar]
  22. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307–1320 [View Article] [PubMed]
     [Google Scholar]
  23. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  24. Grant JR, Enns E, Marinier E, Mandal A, Herman EK et al. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res 2023; 51:W484–W492 [View Article] [PubMed]
     [Google Scholar]
  25. 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] [PubMed]
     [Google Scholar]
  26. 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] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [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] [PubMed]
     [Google Scholar]
  29. Bertelli C, Laird MR, Williams KP, Lau BY. Simon Fraser University Research Computing Group 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]
  30. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–6 [View Article] [PubMed]
     [Google Scholar]
  31. Wishart DS, Han S, Saha S, Oler E, Peters H et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res 2023; 51:W443–W450 [View Article] [PubMed]
     [Google Scholar]
  32. Kanehisa M, Sato Y, Morishima K. lastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  33. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [View Article]
     [Google Scholar]
  34. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article] [PubMed]
     [Google Scholar]
  35. Gschwind R, Ugarcina Perovic S, Weiss M, Petitjean M, Lao J et al. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. Nucleic Acids Res 2023; 51:W493–W500 [View Article] [PubMed]
     [Google Scholar]
  36. Mungan MD, Alanjary M, Blin K, Weber T, Medema MH et al. ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res 2020; 48:W546–W552 [View Article] [PubMed]
     [Google Scholar]
  37. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. AntiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  38. Jeckelmann J-M, Erni B. Carbohydrate transport by group translocation: the bacterial phosphoenolpyruvate: sugar phosphotransferase system. In Kuhn A. ed Bacterial Cell Walls and Membranes Cham: Springer International Publishing; 2019 pp 223–274
     [Google Scholar]
  39. Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022; 40:1023–1025 [View Article] [PubMed]
     [Google Scholar]
  40. Cox DJ, Henick-Kling T. Chemiosmotic energy from malolactic fermentation. J Bacteriol 1989; 171:5750–5752 [View Article] [PubMed]
     [Google Scholar]
  41. Savijoki K, Ingmer H, Varmanen P. Proteolytic systems of lactic acid bacteria. Appl Microbiol Biotechnol 2006; 71:394–406 [View Article] [PubMed]
     [Google Scholar]
  42. Dušková M, Morávková M, Mrázek J, Florianová M, Vorlová L et al. Assessment of antibiotic resistance in starter and non-starter lactobacilli of food origin. Acta Vet Brno 2020; 89:401–411 [View Article]
     [Google Scholar]
  43. Nawaz M, Wang J, Zhou A, Ma C, Wu X et al. Characterization and transfer of antibiotic resistance in lactic acid bacteria from fermented food products. Curr Microbiol 2011; 62:1081–1089 [View Article] [PubMed]
     [Google Scholar]
  44. George NL, Bennett EC, Orlando BJ. Guarding the walls: the multifaceted roles of Bce modules in cell envelope stress sensing and antimicrobial resistance. J Bacteriol 2024; 206:e0012324 [View Article] [PubMed]
     [Google Scholar]
  45. Revilla-Guarinos A, Gebhard S, Mascher T, Zúñiga M. Defence against antimicrobial peptides: different strategies in Firmicutes. Environ Microbiol 2014; 16:1225–1237 [View Article] [PubMed]
     [Google Scholar]
  46. Revilla-Guarinos A, Gebhard S, Alcántara C, Staron A, Mascher T et al. Characterization of a regulatory network of peptide antibiotic detoxification modules in Lactobacillus casei BL23. Appl Environ Microbiol 2013; 79:3160–3170 [View Article] [PubMed]
     [Google Scholar]
  47. Revilla-Guarinos A, Zhang Q, Loderer C, Alcántara C, Müller A et al. ABC Transporter DerAB of Lactobacillus casei mediates resistance against insect-derived defensins. Appl Environ Microbiol 2020; 86:e00818–00820 [View Article] [PubMed]
     [Google Scholar]
  48. Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res 2015; 43:W401–7 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006654
Loading
Holzapfeliella saturejae sp. nov. isolated from flowers of winter savoury Satureja montana L.
Int J Syst Evol Microbiol 75, 006654 (2025); https://doi.org/10.1099/ijsem.0.006654
/content/journal/ijsem/10.1099/ijsem.0.006654
/content/journal/ijsem/10.1099/ijsem.0.006654
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