We are hiring!

Strain identifier

BacDive ID: 134302

Type strain: Yes

Species: Spirosoma rigui

Strain Designation: WPCB118

Strain history: <- KS Baik, MicroID, Co. Ltd.

NCBI tax ID(s): 564064 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 7.1 (current version)

General

@ref: 32316

BacDive-ID: 134302

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Spirosoma rigui WPCB118 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from freshwater .

NCBI tax id

  • NCBI tax id: 564064
  • Matching level: species

strain history: <- KS Baik, MicroID, Co. Ltd.

doi: 10.13145/bacdive134302.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Spirosoma
  • species: Spirosoma rigui
  • full scientific name: Spirosoma rigui Baik et al. 2007

@ref: 32316

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Spirosoma

species: Spirosoma rigui

strain designation: WPCB118

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32316negative6.15 µm0.9 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative
69480negative99.328

pigmentation

  • @ref: 32316
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32316positivegrowth04-37
32316positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32316positivegrowth06-11alkaliphile
32316positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32316facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
32316no
67771no
69480no96.858

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
32316NaClpositivegrowth0-1 %
69480non-halophilic96.817

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3231617234glucose+carbon source
323164853esculin+hydrolysis

enzymes

  • @ref: 32316
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32316freshwater (river, lake, pond)
67771From freshwaterWoopo wetlandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_788.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_148;96_478;97_546;98_629;99_788&stattab=map
  • Last taxonomy: Spirosoma rigui subclade
  • 16S sequence: EF507900
  • Sequence Identity:
  • Total samples: 3439
  • soil counts: 639
  • aquatic counts: 613
  • animal counts: 1274
  • plant counts: 913

Sequence information

16S sequences

  • @ref: 32316
  • description: Spirosoma rigui strain WPCB118 16S ribosomal RNA gene, partial sequence
  • accession: EF507900
  • length: 1407
  • database: nuccore
  • NCBI tax ID: 564064

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Spirosoma rigui KCTC 12531GCA_002067135completencbi564064
66792Spirosoma rigui strain KCTC 12531564064.4completepatric564064

GC content

  • @ref: 32316
  • GC-content: 53.3

External links

@ref: 32316

culture collection no.: KCTC 12531, NBRC 101117

straininfo link

  • @ref: 20218
  • passport: http://www.straininfo.net/strains/764548

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048741Spirosoma rigui sp. nov., isolated from fresh water.Baik KS, Kim MS, Park SC, Lee DW, Lee SD, Ka JO, Choi SK, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65302-02007Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Korea, Locomotion/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny19196773Spirosoma panaciterrae sp. nov., isolated from soil.Ten LN, Xu JL, Jin FX, Im WT, Oh HM, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.002436-02009Cytophagaceae/chemistry/*classification/genetics/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Phylogeny24748440Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.Lee JJ, Srinivasan S, Lim S, Joe M, Im S, Bae SI, Park KR, Han JH, Park SH, Joo BM, Park SJ, Kim MKCurr Microbiol10.1007/s00284-014-0584-x2014Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/*classification/*isolation & purification/physiology/radiation effects, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Gamma Rays, Korea, Locomotion, Microbial Viability/*radiation effects, Microscopy, Electron, Transmission, Molecular Sequence Data, Oryza, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ultraviolet RaysGenetics
Phylogeny26115990Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.Lee JJ, Kang MS, Joo ES, Kim MK, Im WT, Jung HY, Srinivasan SJ Microbiol10.1007/s12275-015-5008-52015Altitude, Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/growth & development/*isolation & purification/radiation effects, DNA, Ribosomal/genetics, *Gamma Rays, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, *Ultraviolet Rays, Vitamin K 2/analogs & derivatives/chemistryPhenotype
Phylogeny29362880Spirosoma agri sp. nov., Isolated from Apple Orchard Soil.Li W, Lee SY, Kang IK, Ten LN, Jung HYCurr Microbiol10.1007/s00284-018-1434-z2018Base Composition/genetics, Cytophagaceae/classification/*genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, *Malus, Phenotype, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny33729126Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica.Tahon G, Lebbe L, Willems AInt J Syst Evol Microbiol10.1099/ijsem.0.0047542021

Reference

@idauthorstitledoi/urljournalpubmedID_cross_reference
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
2855310.1099/ijs.0.65302-018048741
32316Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604128553
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes