Strain identifier

BacDive ID: 24011

Type strain: Yes

Species: Flammeovirga kamogawensis

Strain Designation: YS10

Strain history: IAM 15451 <-- S. Hosoya and A. Yokota YS10.

NCBI tax ID(s): 373891 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20563

BacDive-ID: 24011

DSM-Number: 26273

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Flammeovirga kamogawensis YS10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.

NCBI tax id

  • NCBI tax id: 373891
  • Matching level: species

strain history

@refhistory
20563<- JCM <- IAM <- S. Hosoya and A. Yokota, Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan; YS10
67770IAM 15451 <-- S. Hosoya and A. Yokota YS10.

doi: 10.13145/bacdive24011.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flammeovirgaceae
  • genus: Flammeovirga
  • species: Flammeovirga kamogawensis
  • full scientific name: Flammeovirga kamogawensis Hosoya and Yokota 2007

@ref: 20563

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flammeovirgaceae

genus: Flammeovirga

species: Flammeovirga kamogawensis

full scientific name: Flammeovirga kamogawensis Hosoya and Yokota 2007

strain designation: YS10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32110negative02-40 µm0.6-1 µmrod-shapedyesgliding
69480negative99.911

pigmentation

  • @ref: 32110
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20563
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20563positivegrowth28mesophilic
32110positivegrowth15-30
32110positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
32110positivegrowth06-08
32110positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32110
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32110no
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
32110NaClpositivegrowth02-04 %
32110NaClpositiveoptimum3 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3211017057cellobiose+carbon source
3211028260galactose+carbon source
3211017234glucose+carbon source
3211017716lactose+carbon source
3211017306maltose+carbon source
3211037684mannose+carbon source
3211017632nitrate+reduction

enzymes

  • @ref: 32110
  • value: alkaline phosphatase
  • activity: +
  • ec: 3.1.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20563coastal seawaterKamogawa, YoshiuraJapanJPNAsia
67770Coastal seawater off YoshiuraKamogawaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_45735.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16066;96_20929;97_26070;98_33127;99_45735&stattab=map
  • Last taxonomy: Flammeovirga kamogawensis subclade
  • 16S sequence: AB251933
  • Sequence Identity:
  • Total samples: 618
  • soil counts: 4
  • aquatic counts: 571
  • animal counts: 43

Safety information

risk assessment

  • @ref: 20563
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20563
  • description: Flammeovirga kamogawensis gene for 16S rRNA, partial sequence, strain: YS10
  • accession: AB251933
  • length: 1466
  • database: ena
  • NCBI tax ID: 373891

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flammeovirga kamogawensis YS10GCA_018736065completencbi373891
66792Flammeovirga kamogawensis YS10GCA_007097495contigncbi373891
66792Flammeovirga kamogawensis DSM 26273GCA_014207545scaffoldncbi373891
66792Flammeovirga kamogawensis strain DSM 26273373891.5wgspatric373891
66792Flammeovirga kamogawensis strain YS10373891.4wgspatric373891
66792Flammeovirga kamogawensis DSM 262732861514905draftimg373891

GC content

@refGC-contentmethod
2056332-33high performance liquid chromatography (HPLC)
3211032-33

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno91.841yes
gram-positiveno98.389no
anaerobicno96.879yes
aerobicyes79.245yes
halophileno79.413no
spore-formingno91.162yes
thermophileno97.821yes
motileno84.828no
glucose-utilyes85.026no
glucose-fermentno78.329no

External links

@ref: 20563

culture collection no.: DSM 26273, IAM 15451, JCM 23196, NCIMB 14281

straininfo link

  • @ref: 87985
  • straininfo: 309447

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551052
  • title: Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan.
  • authors: Hosoya S, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64977-0
  • year: 2007
  • mesh: Agar/metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Japan, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20563Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26273Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26273)
32110Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172835528776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87985Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID309447.1