Strain identifier

BacDive ID: 139541

Type strain: No

Species: Flavobacterium columnare

Strain history: CIP <- 1993, ATCC <- 1992, J.F. Bernardet, INRA, Jouy en Josas, France: strain TG 44/87, Flexibacter columnaris

NCBI tax ID(s): 1041826 (strain), 996 (species)

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General

@ref: 41892

BacDive-ID: 139541

keywords: genome sequence, Bacteria, psychrophilic, Gram-negative

description: Flavobacterium columnare CIP 103533 is a psychrophilic, Gram-negative bacterium of the family Flavobacteriaceae.

NCBI tax id

NCBI tax idMatching level
1041826strain
996species

strain history

  • @ref: 41892
  • history: CIP <- 1993, ATCC <- 1992, J.F. Bernardet, INRA, Jouy en Josas, France: strain TG 44/87, Flexibacter columnaris

doi: 10.13145/bacdive139541.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium columnare
  • full scientific name: Flavobacterium columnare (Bernardet and Grimont 1989 ex Davis 1922) Bernardet et al. 1996

  • synonyms

    @refsynonym
    20215Cytophaga columnaris
    20215Flexibacter columnaris

@ref: 41892

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium columnare

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.997
41892negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41892MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
41892CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
41892CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
41892positivegrowth22psychrophilic
41892positivegrowth10-37
41892nogrowth5psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4189217632nitrate-reduction
4189216301nitrite-reduction
41892132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 41892
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
41892oxidase+
41892beta-galactosidase-3.2.1.23
41892gelatinase+
41892caseinase-3.4.21.50
41892catalase+1.11.1.6
41892lipase-
41892urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
41892Villedieu-les-PoelesFranceFRAEurope
41892Villedieu les PoêlesFranceFRAEuropeAnimal, Brown trout fry, skin lesions1987

Safety information

risk assessment

  • @ref: 41892
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium columnare ATCC 49512GCA_000240075completencbi1041826
66792Flavobacterium columnare ATCC 495121041826.3completepatric1041826
66792Flavobacterium columnare ATCC 495122511231122completeimg1041826

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.478no
flagellatedno95.681no
gram-positiveno98.84no
anaerobicno98.65no
aerobicyes84.098no
halophileno93.448no
spore-formingno95.176no
thermophileno97.506no
glucose-utilyes69.743no
glucose-fermentno92.488no

External links

@ref: 41892

culture collection no.: CIP 103533, ATCC 49512

straininfo link

  • @ref: 96023
  • straininfo: 42527

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics22535941Genome sequence of the fish pathogen Flavobacterium columnare ATCC 49512.Tekedar HC, Karsi A, Gillaspy AF, Dyer DW, Benton NR, Zaitshik J, Vamenta S, Banes MM, Gulsoy N, Aboko-Cole M, Waldbieser GC, Lawrence MLJ Bacteriol10.1128/JB.00281-122012Animals, Fish Diseases/*microbiology, Fishes, Flavobacterium/*classification/*genetics, Gene Library, *Genome, Bacterial, Molecular Sequence DataPhylogeny
Genetics28469601Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512.Tekedar HC, Karsi A, Reddy JS, Nho SW, Kalindamar S, Lawrence MLFront Microbiol10.3389/fmicb.2017.005882017
28790987Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes.Kumru S, Tekedar HC, Gulsoy N, Waldbieser GC, Lawrence ML, Karsi AFront Microbiol10.3389/fmicb.2017.013752017
Pathogenicity33276599Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen.Laanto E, Ravantti JJ, Sundberg LRMicroorganisms10.3390/microorganisms81219192020

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
41892Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103533Collection of Institut Pasteur (CIP 103533)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
96023Reimer, 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-ID42527.1