Strain identifier

BacDive ID: 5551

Type strain: Yes

Species: Flavobacterium columnare

Strain Designation: 1-S-2cl (Anacker 1956)

Strain history: CIP <- 1993, NCIMB <- E.J. Ordal, Washington Univ., Seattle, USA: strain 1-S-2cl, Cytophaga columnaris

NCBI tax ID(s): 1218111 (strain), 996 (species)

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General

@ref: 7633

BacDive-ID: 5551

DSM-Number: 18644

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile, rod-shaped, colony-forming, animal pathogen

description: Flavobacterium columnare 1-S-2cl is a psychrophilic, motile, rod-shaped animal pathogen that forms rhizoid colonies and was isolated from Kidney of diseased salmon.

NCBI tax id

NCBI tax idMatching level
1218111strain
996species

strain history

@refhistory
7633<- CIP <- E. J. Ordal, Univ. of Washington, Seattle, USA; 1-S-2cl (Anacker 1956)
67770IAM 14301 <-- NCIMB 2248 <-- E. J. Ordal I-S-2cl.
118709CIP <- 1993, NCIMB <- E.J. Ordal, Washington Univ., Seattle, USA: strain 1-S-2cl, Cytophaga columnaris

doi: 10.13145/bacdive5551.20230509.8.1

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: 7633

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium columnare

full scientific name: Flavobacterium columnare (Bernardet and Grimont 1989) Bernardet et al. 1996

strain designation: 1-S-2cl (Anacker 1956)

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityflagellum arrangementgram stain
433433-10 µm0.3-0.5 µmrod-shapedyesgliding
118709rod-shapednonegative

colony morphology

  • @ref: 43343
  • colony color: greenish-yellow
  • colony shape: rhizoid
  • medium used: Anacker and Ordal's agar

pigmentation

  • @ref: 43343
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7633R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
7633ENRICHED CYTOPHAGA AGAR MEDIUM (DSMZ Medium 1133)yeshttps://mediadive.dsmz.de/medium/1133Name: ENRICHED CYTOPHAGA AGAR MEDIUM (DSMZ Medium 1133) Composition: Agar 15.0 g/l Tryptone 2.0 g/l Yeast extract 0.5 g/l Beef extract 0.5 g/l Sodium acetate 0.2 g/l Distilled water
40693MEDIUM 34 - for Flavobacterium branchiophilum and Flavobacterium columnareyesDistilled water make up to (1000.000 ml);Agar (10.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (0.500 g);Beef extract (0.200 g)
43343Marine agar (MA)no
43343Tryptic Soy Agarno
43343Anacker and Ordal's agaryes
118709CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7633positivegrowth15psychrophilic
40693positivegrowth22psychrophilic
43343positiveoptimum25-30mesophilic
43343positivegrowth15-37
67770positivegrowth20psychrophilic
118709positivegrowth15-30
118709nogrowth5psychrophilic
118709nogrowth10psychrophilic
118709nogrowth37mesophilic

Physiology and metabolism

spore formation

  • @ref: 43343
  • type of spore: endospore
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43343NaClpositivegrowth0-0.5 %(w/v)
43343NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433432509agar-degradation
4334328938ammonium-nitrogen source
4334385146carboxymethylcellulose-degradation
43343casein+degradation
4334317029chitin-degradation
4334316991dna+degradation
433434853esculin-degradation
433435291gelatin+degradation
4334317234glucose-assimilation
4334317632nitrate-nitrogen source
4334328017starch+degradation
4334353424tween 20+degradation
4334353423tween 40+degradation
4334353425tween 60+degradation
4334353426tween 80+degradation
4334316199urea-degradation
1187094853esculin-hydrolysis
11870917632nitrate-reduction
11870916301nitrite-reduction
118709132112sodium thiosulfate+builds gas from

antibiotic resistance

  • @ref: 118709
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
4334316136hydrogen sulfideyes
11870935581indoleno

enzymes

@refvalueactivityec
43343catalase+1.11.1.6
43343arginine dihydrolase-3.5.3.6
43343lysine decarboxylase-4.1.1.18
43343ornithine decarboxylase-4.1.1.17
43343cytochrome oxidase+1.9.3.1
43343beta-galactosidase-3.2.1.23
118709oxidase-
118709beta-galactosidase-3.2.1.23
118709alcohol dehydrogenase-1.1.1.1
118709gelatinase+
118709amylase-
118709DNase-
118709caseinase+3.4.21.50
118709catalase+1.11.1.6
118709gamma-glutamyltransferase+2.3.2.2
118709lecithinase-
118709lipase-
118709lysine decarboxylase-4.1.1.18
118709ornithine decarboxylase-4.1.1.17
118709urease-3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118709---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost speciesisolation date
7633Kidney of diseased salmonWashington, Snake RiverUSAUSANorth America
67770Kidney of a diseased chinook salmon (Oncorhynchus tschawytscha) from the Snake RiverWAUSAUSANorth AmericaOncorhynchus tschawytscha
118709Animal, Salmon, kidneySnake river, WashingtonUnited States of AmericaUSANorth America1955

isolation source categories

Cat1Cat2Cat3
#Host#Fishes#Salmonidae
#Host Body-Site#Urogenital tract#Kidney

taxonmaps

  • @ref: 69479
  • File name: preview.99_3559.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1022;97_1192;98_1427;99_3559&stattab=map
  • Last taxonomy: Flavobacterium columnare subclade
  • 16S sequence: KC912654
  • Sequence Identity:
  • Total samples: 7090
  • soil counts: 1205
  • aquatic counts: 4062
  • animal counts: 1474
  • plant counts: 349

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7633yes1Risk group (German classification)
1187091Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium columnare strain ATCC 23463 16S ribosomal RNA gene, partial sequenceAY577821517ena996
20218Flavobacterium columnare strain ATCC 23463 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY754372576ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-5 16S ribosomal RNA gene, partial sequenceKC9126471254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-14 16S ribosomal RNA gene, partial sequenceKC9126481254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-11 16S ribosomal RNA gene, partial sequenceKC9126491254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-16 16S ribosomal RNA gene, partial sequenceKC9126501254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-1 16S ribosomal RNA gene, partial sequenceKC9126511254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-7 16S ribosomal RNA gene, partial sequenceKC9126521254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-13 16S ribosomal RNA gene, partial sequenceKC9126531254ena996
20218Flavobacterium columnare strain ATCC 23463 clone GI-10 16S ribosomal RNA gene, partial sequenceKC9126541254ena996
20218Flavobacterium columnare gene for 16S rRNA, partial sequence, strain: IAM 14301 (= NCMB 2248)AB0109511478ena996
20218Flavobacterium columnare DNA, 16S-23S intergenic spacer region, complete sequenceAB030748635ena996
20218Flavobacterium columnare gene for 16S rRNA, strain:IFO 15943AB0780471471ena996
20218Flavobacterium columnare gene for 16S rRNA, partial sequence, strain: NBRC 100251AB6811501441ena996
20218Flavobacterium columnare gene for 16S ribosomal RNA, partial sequence, strain: NCIMB 2248D126591256ena996

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium columnare NBRC 100251 = ATCC 23463GCA_007990835contigncbi1218111
66792Flavobacterium columnare NBRC 100251 = ATCC 23463GCA_002530675scaffoldncbi1218111
66792Flavobacterium columnare NBRC 100251 = ATCC 234631218111.3wgspatric1218111
66792Flavobacterium columnare strain ATCC 23463996.48wgspatric996
66792Flavobacterium columnare strain ATCC 23463996.64wgspatric996

GC content

@refGC-contentmethod
763332
4334332-33thermal denaturation, midpoint method (Tm)
6777030Buoyant density centrifugation (BD)
6777032thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.103yes
gram-positiveno98.916no
anaerobicno98.52no
aerobicyes83.046no
halophileno93.268yes
spore-formingno95.093yes
thermophileno97.778no
glucose-utilyes65.981yes
motileno90.629no
glucose-fermentno92.657no

External links

@ref: 7633

culture collection no.: DSM 18644, ATCC 23463, CIP 103531, JCM 21141, LMG 10406, LMG 13035, NBRC 100251, NCIMB 2248, IAM 14301, NCMB 1038

straininfo link

  • @ref: 75033
  • straininfo: 9858

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
15482422Systemic and mucosal antibody response in tilapia, Oreochromis niloticus (L.), following immunization with Flavobacterium columnare.Grabowski LD, LaPatra SE, Cain KDJ Fish Dis10.1111/j.1365-2761.2004.00576.x2004Animals, Antibodies, Bacterial/blood, Antibody Formation/*immunology, Cichlids/*immunology, Enzyme-Linked Immunosorbent Assay/veterinary, *Flavobacterium, Freund's Adjuvant/immunology, Immersion, Immunity, Mucosal/*immunology, Immunization/*veterinary, Injections, Intraperitoneal/veterinary, Time Factors
16449454Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment.Wang ZW, Liu YH, Dai X, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64065-02006Bacterial Typing Techniques, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhylogenyGenetics
16875391Molecular diversity and growth features of Flavobacterium columnare strains isolated in Finland.Suomalainen LR, Kunttu H, Valtonen ET, Hirvela-Koski V, Tiirola MDis Aquat Organ10.3354/dao0700552006Animals, DNA, Ribosomal Spacer/genetics, Finland, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Flavobacterium/drug effects/*genetics/*growth & development/isolation & purification, *Genetic Variation, Hydrogen-Ion Concentration, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride, TemperaturePhylogenyGenetics
17625200Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64935-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyPhylogenyGenetics
19306607Improved method for determining antibiotic susceptibility of Flavobacterium columnare isolates by broth microdilution.Darwish AM, Farmer BD, Hawke JPJ Aquat Anim Health10.1577/H07-047.12008Animals, Anti-Bacterial Agents/*pharmacology, Colony Count, Microbial/veterinary, Culture Media, Dose-Response Relationship, Drug, *Drug Resistance, Bacterial, Fish Diseases/*drug therapy/microbiology, Fishes, Flavobacteriaceae Infections/drug therapy/microbiology/*veterinary, Flavobacterium/*drug effects/genetics/growth & development, Genotype, Microbial Sensitivity Tests/methods/standards/veterinary, Temperature, Time Factors, Treatment OutcomeCultivationGenetics
25773973Improving survival and storage stability of bacteria recalcitrant to freeze-drying: a coordinated study by European culture collections.Peiren J, Buyse J, De Vos P, Lang E, Clermont D, Hamon S, Begaud E, Bizet C, Pascual J, Ruvira MA, Macian MC, Arahal DRAppl Microbiol Biotechnol10.1007/s00253-015-6476-62015Bacterial Physiological Phenomena/*radiation effects, Biological Specimen Banks, Freeze Drying/*methods, Microbial Viability/*radiation effects, Preservation, Biological/*methods
33276599Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen.Laanto E, Ravantti JJ, Sundberg LRMicroorganisms10.3390/microorganisms81219192020Pathogenicity
35026686The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare.LaFrentz BR, Kralova S, Burbick CR, Alexander TL, Phillips CW, Griffin MJ, Waldbieser GC, Garcia JC, de Alexandre Sebastiao F, Soto E, Loch TP, Liles MR, Snekvik KRSyst Appl Microbiol10.1016/j.syapm.2021.1262932021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Flavobacterium, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhylogenyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7633Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18644)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18644
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40693Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15339
4334310.1007/978-0-387-68572-4
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75033Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9858.1StrainInfo: A central database for resolving microbial strain identifiers
118709Curators of the CIPCollection of Institut Pasteur (CIP 103531)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103531