1887

Abstract

A novel Gram-stain-positive, facultatively anaerobic, non-motile, catalase-positive, oxidase-negative and ovoid cocci, designated as A1S7, was isolated from the gut of a marine sandworm (). Strain A1S7 exhibited optimal growth at temperatures of 20–30 ℃, pH 6–8 and in the presence of 2–4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain A1S7 belonged to the genus , exhibiting a similarity of 99.0% to KCTC 49873, followed by KCTC 19282 (98.8%), KCTC 49872 (98.4%), KACC 20518 (98.2%) and KACC 21120 (97.2%). The complete genome sequence of strain A1S7 revealed a genome size of 3360920 bp with a genomic G+C content of 70.1 mol%. The orthologous average nucleotide identity and the digital DNA–DNA hybridization values between strain A1S7 and KCTC 49873 were determined to be 89.5 and 37.2%, respectively. The major respiratory quinone was MK-8(H). The predominant fatty acids (>10%) included -C, C 8, C 9 and C. Polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and three unknown polar lipids. The cell-wall peptidoglycan type was A1. The major whole-cell sugars were ribose, mannose and glucose. Based on phenotypic, phylogenetic, genotypic and chemotaxonomic properties, strain A1S7 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is A1S7 (=KCTC 49714 = JCM 36706).

Funding
This study was supported by the:
  • Ministry of Science and ICT, South Korea (Award RS-2023-00211215)
    • Principle Award Recipient: Na-RiShin
  • Korea Research Institute of Bioscience and Biotechnology (Award KGM5232423)
    • Principle Award Recipient: Na-RiShin
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006557
2024-10-25
2024-11-05
Loading full text...

Full text loading...

References

  1. Martin K, Schumann P, Rainey FA, Schuetze B, Groth I. Janibacter limosus gen. nov., sp. nov., a new actinomycete with meso-diaminopimelic acid in the cell wall. Int J Syst Bacteriol 1997; 47:529–534 [View Article] [PubMed]
    [Google Scholar]
  2. Yoon JH, Lee KC, Kang SS, Kho YH, Kang KH et al. Janibacter terrae sp. nov., a bacterium isolated from soil around a wastewater treatment plant. Int J Syst Evol Microbiol 2000; 50:1821–1827 [View Article]
    [Google Scholar]
  3. Yoon JH, Lee HB, Yeo SH, Choi JE. Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea. Int J Syst Evol Microbiol 2004; 54:1975–1980 [View Article]
    [Google Scholar]
  4. Kämpfer P, Terenius O, Lindh JM, Faye I. Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis. Int J Syst Evol Microbiol 2006; 56:389–392 [View Article]
    [Google Scholar]
  5. Kageyama A, Takahashi Y, Yasumoto-Hirose M, Kasai H, Shizuri Y et al. Janibacter corallicola sp. nov., isolated from coral in Palau. J Gen Appl Microbiol 2007; 53:185–189 [View Article]
    [Google Scholar]
  6. Shivaji S, Chaturvedi P, Begum Z, Pindi PK, Manorama R et al. Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere. Int J Syst Evol Microbiol 2009; 59:2977–2986 [View Article] [PubMed]
    [Google Scholar]
  7. Li J, Long L-J, Yang L, Xu Y, Wang F-Z et al. Janibacter alkaliphilus sp. nov., isolated from coral Anthogorgia sp. Antonie van Leeuwenhoek 2012; 102:157–162 [View Article]
    [Google Scholar]
  8. Hamada M, Shibata C, Tamura T, Yamamura H, Hayakawa M et al. Janibacter cremeus sp. nov., an actinobacterium isolated from sea sediment. Int J Syst Evol Microbiol 2013; 63:3687–3690 [View Article] [PubMed]
    [Google Scholar]
  9. Zhang G, Ren H, Wang S, Chen X, Yang Y et al. Janibacter indicus sp. nov., isolated from hydrothermal sediment of the Indian Ocean. Int J Syst Evol Microbiol 2014; 64:2353–2357 [View Article] [PubMed]
    [Google Scholar]
  10. Zhang Z, Zhou E-M, Li C-J, Jiang X-W, Mao R-F et al. Janibacter endophyticus sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. Yunnanensis. Curr Microbiol 2022; 79:1–6 [View Article]
    [Google Scholar]
  11. Yang AI, Joe HI, Choe H, Kim HS, Eom MK et al. Alkalimarinus alittae sp. nov., isolated from gut of marine sandworm (Alitta virens) and emended description of the genus Alkalimarinus. Int J Syst Evol Microbiol 2023; 73:1–9
    [Google Scholar]
  12. Shin N-R, Kang W, Tak EJ, Hyun D-W, Kim PS et al. Blautia hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1059–1064 [View Article]
    [Google Scholar]
  13. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 1985; 82:6955–6959 [View Article] [PubMed]
    [Google Scholar]
  14. Chalita M, Kim YO, Park S, Oh H-S, Cho JH et al. EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol 2024; 74:006421 [View Article] [PubMed]
    [Google Scholar]
  15. Hall TA, Biosciences I, Carlsbad C. BioEdit: an important software for molecular biology. GERF Bull Biosci 2011; 2:60–61
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  19. 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]
  20. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  24. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
    [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genom 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  26. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525
    [Google Scholar]
  27. Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic acids Res 2022; 50:D912–D917 [View Article]
    [Google Scholar]
  28. Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P et al. Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genom 2011; 12:383 [View Article]
    [Google Scholar]
  29. Cerdeño-Tárraga AM, Efstratiou A, Dover LG, Holden MTG, Pallen M et al. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res 2003; 31:6516–6523 [View Article] [PubMed]
    [Google Scholar]
  30. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758
    [Google Scholar]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI inc; 1990
    [Google Scholar]
  32. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  33. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354
    [Google Scholar]
  34. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. In Methods in Microbiology Elsevier; 1988 pp 161–207 [View Article]
    [Google Scholar]
  35. 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]
/content/journal/ijsem/10.1099/ijsem.0.006557
Loading
/content/journal/ijsem/10.1099/ijsem.0.006557
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