Skip to content
1887

Abstract

Three bacterial strains, designated FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic and phylogenomic analysis places them within the genus . Strains FBOR7N2.3 and FZUR7N2.5 share 100% of similarity in the 16S rRNA gene sequence, and both are most closely related to AR-3-4 with which they share 97.5% of 16S rRNA gene similarity. Strain FZUC8N2.13 forms a distinct lineage most closely related to IMCC36792 with 97.7% 16S rRNA gene similarity. The closest phylogenomic neighbours of these three strains are DSM 1076, ‘’ BBQ-18 and PK15. The average nucleotide identity and digital DNA–DNA hybridization values between the three strains and closest members of the genus are below the threshold values of 95% and 70%, respectively. Strains FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5 stain Gram-negative, are rod-shaped and form yellow colonies. Optimum growth occurs at 25 °C and pH 7. The genomic G+C contents are 33.4 mol% for strain FZUC8N2.13 and 33.2 mol% for strains FBOR7N2.3 and FZUR7N2.5. The major isoprenoid quinone is menaquinone 6. The major fatty acids are summed feature 3 (C ω7c and/or C ω6c) (22.6–31.1%), iso-C (13.6–16.2 %) and anteiso-C (8.7–10.5%). The polar lipids consist of two aminolipids, two aminophospholipids and one glycolipid. The phylogenetic, phylogenomic, phenotypic and chemotaxonomic data indicate that FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5 are distinct from the described species of and should be classified as novel species, for which we propose the names for strain FZUC8N2.13 (=UCCCB 179=CECT 30977) and for strains FBOR7N2.3 (=UCCCB 178=CECT 30976) and FZUR7N2.5 (=UCCCB 216=CECT 31036).

Funding
This study was supported by the:
  • Next Generation EU, Resilience and Recovery Plan (Award "AM2R", reference: 7253)
    • Principal Award Recipient: PaulaV. Morais
  • Horizon 2020 ERA-NET/ERA-MIN (Award ERA-MIN/0007/2019; Grant nº67)
    • Principal Award Recipient: PaulaV. Morais
  • Horizon 2020 (Award Grant nº821096)
    • Principal Award Recipient: PaulaV. Morais
  • Fundação para a Ciência e a Tecnologia (Award LA/P/0112/2020)
    • Principal Award Recipient: NotApplicable
  • Fundação para a Ciência e a Tecnologia (Award UID/EMS/00285/2020)
    • Principal Award Recipient: NotApplicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006660
2025-01-28
2026-02-11

Metrics

Loading full text...

Full text loading...

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FMG II. Flavobacterium gen. nov. In Whitman W. eds Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923 pp 97–117
    [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  3. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 2013; 63:886–892 [View Article] [PubMed]
    [Google Scholar]
  4. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article] [PubMed]
    [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai’i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article] [PubMed]
    [Google Scholar]
  6. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  7. Chaudhary DK, Khulan A, Kim D-U, Kim J. Flavobacterium cellulosilyticum sp. nov., a novel psychrophilic bacterium isolated from Arctic soil. Int J Syst Evol Microbiol 2020; 70:44–50 [View Article] [PubMed]
    [Google Scholar]
  8. Yi H, Chun J. Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic. Int J Syst Evol Microbiol 2006; 56:1239–1244 [View Article]
    [Google Scholar]
  9. Van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 2004; 54:85–92 [View Article] [PubMed]
    [Google Scholar]
  10. Lee Y, Jeon CO. Flavobacterium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:1919–1924 [View Article] [PubMed]
    [Google Scholar]
  11. Lee SH, Kim JM, Lee JR, Park W, Jeon CO. Flavobacterium fluvii sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2010; 60:353–357 [View Article]
    [Google Scholar]
  12. Chen W-M, Chen J-C, Sheu S-Y. Flavobacterium oryzae sp. nov., isolated from a flooded rice field, and emended descriptions of Flavobacterium flevense, Flavobacterium yonginense and Flavobacterium myungsuense. Int J Syst Evol Microbiol 2014; 64:3701–3708 [View Article] [PubMed]
    [Google Scholar]
  13. Kim DH, Singh P, Farh ME-A, Kim Y-J, Nguyen N-L et al. Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng. Antonie Van Leeuwenhoek 2016; 109:1199–1208 [View Article] [PubMed]
    [Google Scholar]
  14. Menon RR, Kumari S, Viver T, Rameshkumar N. Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala. Microbiol Res 2020; 240:126533 [View Article] [PubMed]
    [Google Scholar]
  15. Yang L-L, Liu Q, Liu H-C, Zhou Y-G, Xin Y-H. Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:1821–1825 [View Article] [PubMed]
    [Google Scholar]
  16. Zhang D-C, Wang H-X, Liu H-C, Dong X-Z, Zhou P-J. Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 2006; 56:2921–2925 [View Article] [PubMed]
    [Google Scholar]
  17. Aslam Z, Im W-T, Kim MK, Lee S-T. Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. Int J Syst Evol Microbiol 2005; 55:747–751 [View Article] [PubMed]
    [Google Scholar]
  18. Miyashita M, Fujimura S, Nakagawa Y, Nishizawa M, Tomizuka N et al. Flavobacterium algicola sp. nov., isolated from marine algae. Int J Syst Evol Microbiol 2010; 60:344–348 [View Article] [PubMed]
    [Google Scholar]
  19. Nam GG, Joung Y, Park M, Kim S, Jeon HT et al. Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake. Int J Syst Evol Microbiol 2017; 67:2440–2445 [View Article] [PubMed]
    [Google Scholar]
  20. Ahn J-H, Kim TW, Kim T-S, Joung Y, Kim SB. Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater. Int J Syst Evol Microbiol 2017; 67:3117–3121 [View Article] [PubMed]
    [Google Scholar]
  21. Králová S, Busse H-J, Švec P, Mašlaňová I, Staňková E et al. Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples. Syst Appl Microbiol 2019; 42:291–301 [View Article] [PubMed]
    [Google Scholar]
  22. Millar WN. Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples. Syst Appl Microbiol 1973; 23:142–150 [View Article]
    [Google Scholar]
  23. Chen W-M, Yang C-C, Sheu C, Kwon S-W, Sheu S-Y. Flavobacterium ichthyis sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2020; 70:5075–5086 [View Article] [PubMed]
    [Google Scholar]
  24. Morais PV, Francisco R, Branco R, Chung AP, da Costa MS. Leucobacter chromiireducens sp. nov, and Leucobacter aridicollis sp. nov., two new species isolated from a chromium contaminated environment. Syst Appl Microbiol 2004; 27:646–652 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–6 [View Article] [PubMed]
    [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  31. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
    [Google Scholar]
  35. 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]
  36. 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]
  37. Kim J, Na S-I, Kim D, Chun J. UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
    [Google Scholar]
  40. Smibert RM, Krieg NR. General characterization. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. eds Manual of Methods for General Bacteriology Washington, D.C., USA: American Society for Microbiology; 1981 pp 411–442
    [Google Scholar]
  41. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  42. da Costa MS, Nobre MF, Wait R. Analysis of lipids from extremophilic Bacteria. In Methods in Microbiology vol 35 Academic Press; 2006 pp 127–159 https://doi.org/10.1016/S0580-9517(08)70009-6.Academic
    [Google Scholar]
  43. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, Delaware, USA: MIDI inc; 1990
    [Google Scholar]
  44. 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]
  45. Padan E, Bibi E, Ito M, Krulwich TA. Alkaline pH homeostasis in bacteria: new insights. Biochim Biophys Acta 2005; 1717:67–88 [View Article] [PubMed]
    [Google Scholar]
  46. Rhodes RG, Samarasam MN, Shrivastava A, van Baaren JM, Pochiraju S et al. Flavobacterium johnsoniae gldN and gldO are partially redundant genes required for gliding motility and surface localization of SprB. J Bacteriol 2010; 192:1201–1211 [View Article] [PubMed]
    [Google Scholar]
  47. Hunnicutt DW, McBride MJ. Cloning and characterization of the Flavobacterium johnsoniae gliding-motility genes gldB and gldC. J Bacteriol 2000; 182:911–918 [View Article] [PubMed]
    [Google Scholar]
  48. Hunnicutt DW, McBride MJ. Cloning and characterization of the Flavobacterium johnsoniae gliding motility genes gldD and gldE. J Bacteriol 2001; 183:4167–4175 [View Article] [PubMed]
    [Google Scholar]
  49. Kempf MJ, McBride MJ. Transposon insertions in the Flavobacterium johnsoniae ftsX gene disrupt gliding motility and cell division. J Bacteriol 2000; 182:1671–1679 [View Article] [PubMed]
    [Google Scholar]
  50. McBride MJ, Nakane D. Flavobacterium gliding motility and the type IX secretion system. Curr Opin Microbiol 2015; 28:72–77 [View Article] [PubMed]
    [Google Scholar]
  51. Paillat M, Lunar Silva I, Cascales E, Doan T. A journey with type IX secretion system effectors: selection, transport, processing and activities. Microbiology 2023; 169:001320 [View Article] [PubMed]
    [Google Scholar]
  52. Bartoš O, Chmel M, Swierczková I. The overlooked evolutionary dynamics of 16S rRNA revises its role as the “gold standard” for bacterial species identification. Sci Rep 2024; 14:9067 [View Article]
    [Google Scholar]
  53. Hassler HB, Probert B, Moore C, Lawson E, Jackson RW et al. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. Microbiome 2022; 10:104 [View Article] [PubMed]
    [Google Scholar]
  54. Chen W-M, Xie Y-R, Kwon S-W, Sheu S-Y. Flavobacterium undicola sp. nov., isolated from a freshwater lake. Arch Microbiol 2021; 203:989–1000 [View Article]
    [Google Scholar]
  55. Jo H, Park MS, Lim Y, Kang I, Cho J-C. Ten novel species belonging to the genus Flavobacterium, isolated from freshwater environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre sp. nov., and F. eburneipallidum sp. nov. J Microbiol 2023; 61:495–510 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006660
Loading
/content/journal/ijsem/10.1099/ijsem.0.006660
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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