Strain identifier

BacDive ID: 5529

Type strain: Yes

Species: Flavobacterium psychrophilum

Strain Designation: 3068

Strain history: CIP <- 1993, NCIMB, Flexibacter psychrophilus <- E.J. Ordal, Washington Univ., Seattle, USA

NCBI tax ID(s): 1121894 (strain), 96345 (species)

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General

@ref: 1444

BacDive-ID: 5529

DSM-Number: 3660

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

description: Flavobacterium psychrophilum 3068 is an aerobe, psychrophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from coho salmon Oncorhynchus kitsuch.

NCBI tax id

NCBI tax idMatching level
1121894strain
96345species

strain history

@refhistory
1444<- H. Reichenbach <- NCMB <- G.L. Bullock, 3068 <- E.J. Ordal
67770NCIMB 1947 <-- G. L. Bullock 3068 <-- E. J. Ordal.
122026CIP <- 1993, NCIMB, Flexibacter psychrophilus <- E.J. Ordal, Washington Univ., Seattle, USA

doi: 10.13145/bacdive5529.20230509.8.1

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 psychrophilum
  • full scientific name: Flavobacterium psychrophilum (Bernardet and Grimont 1989 ex Borg 1960) Bernardet et al. 1996

  • synonyms

    @refsynonym
    20215Cytophaga psychrophila
    20215Flexibacter psychrophilus

@ref: 1444

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium psychrophilum

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

strain designation: 3068

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
43348negative1-5 µm0.4-0.5 µmrod-shapedyesgliding
122026rod-shapedno

colony morphology

  • @ref: 43348
  • colony shape: circular

pigmentation

  • @ref: 43348
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1444R2A 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
1444CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
41925MEDIUM 36 - for Flavobacterium psychrophilumyesDistilled water make up to (1000.000 ml);Agar (10.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (5.000 g);Beef extract (0.200 g)
43348Marine agar (MA)no
43348Nutrient agar (NA)yes
43348Tryptic Soy Agarno
122026CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
1444positivegrowth20psychrophilic
41925positivegrowth22psychrophilic
43348positiveoptimum15-20psychrophilic
43348positivegrowth5-23psychrophilic
67770positivegrowth20psychrophilic
122026positivegrowth10-22psychrophilic
122026nogrowth30mesophilic
122026nogrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43348
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43348NaClpositivegrowth0-1 %(w/v)
43348NaClpositiveoptimum0 %(w/v)
122026NaClpositivegrowth0 %
122026NaClnogrowth2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433482509agar-degradation
4334858187alginate-degradation
4334885146carboxymethylcellulose-degradation
43348casamino acids+nitrogen source
43348casein+degradation
4334817029chitin-degradation
4334816991dna+/-degradation
433484853esculin-degradation
433485291gelatin+degradation
4334817234glucose-assimilation
4334861995lecithin+fermentation
4334817632nitrate-reduction
4334817309pectin-degradation
43348peptone+nitrogen source
4334828017starch-degradation
4334835020tributyrin+hydrolysis
4334853424tween 20+degradation
4334853423tween 40+degradation
4334853425tween 60+degradation
4334853426tween 80+degradation
4334816199urea-degradation
1220264853esculin-hydrolysis
12202617632nitrate-reduction
122026132112sodium thiosulfate-builds gas from

antibiotic resistance

  • @ref: 122026
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
4334816136hydrogen sulfideno
4334835581indoleno
12202635581indoleno

enzymes

@refvalueactivityec
43348beta-galactosidase-3.2.1.23
43348cytochrome oxidase+/-1.9.3.1
43348catalase+/-1.11.1.6
43348arginine dihydrolase-3.5.3.6
43348lysine decarboxylase-4.1.1.18
43348ornithine decarboxylase-4.1.1.17
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122026oxidase-
122026beta-galactosidase-3.2.1.23
122026alcohol dehydrogenase-1.1.1.1
122026DNase-
122026catalase-1.11.1.6
122026lysine decarboxylase-4.1.1.18
122026ornithine decarboxylase-4.1.1.17
122026urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122026-+++-+----++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122026---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
1444coho salmon Oncorhynchus kitsuchOncorhynchus kitsuchUSAUSANorth America
67770Coho salmon (Oncorhynchus kitsuch)Oncorhynchus kitsuch
122026Animal, Coho salmon, kidneyUnited States of AmericaUSANorth AmericaWashington

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes
  • Cat3: #Salmonidae

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1444yes1Risk group (German classification)
1220261Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium psychrophilum 16S ribosomal RNA gene, partial sequenceAF0909911424ena96345
20218Flavobacterium psychrophilum strain ATCC 49418 16S ribosomal RNA gene, partial sequenceAY577822513ena96345
20218Flavobacterium psychrophilum strain ATCC 49418 16S ribosomal RNA gene, partial sequenceAY6624931344ena96345
20218Flavobacterium psychrophilum strain ATCC 49418 16S-23S intergenic spacer, partial sequenceAY757361592ena96345
20218Flavobacterium psychrophilum strain DSM 3660 16S ribosomal RNA gene, partial sequenceJX6570451259ena96345
20218Flavobacterium psychrophilum gene for 16S rRNA, partial sequence, strain: NBRC 100250AB6811491437ena96345
20218Flavobacterium psychrophilum gene for 16S ribosomal RNA, partial sequenceD126701256ena96345
20218Flavobacterium psychrophilum 16S ribosomal RNA gene, partial sequenceAY034478478ena96345
4334816S rRNA gene sequenceAB078060nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium psychrophilum DSM 3660 = ATCC 49418GCA_900101925scaffoldncbi1121894
66792Flavobacterium psychrophilum DSM 3660 = ATCC 49418GCA_002217405scaffoldncbi1121894
66792Flavobacterium psychrophilum DSM 36601121894.3wgspatric1121894
66792Flavobacterium psychrophilum strain ATCC 4941896345.93wgspatric96345
66792Flavobacterium psychrophilum DSM 36602622736523draftimg1121894

GC content

@refGC-contentmethod
144431.0
4334832.3-33.8thermal denaturation, midpoint method (Tm)
4334832.3-33.8Buoyant density centrifugation (BD)
6777032Buoyant density centrifugation (BD)
6777032.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.779no
flagellatedno96.381yes
gram-positiveno98.855yes
anaerobicno98.681yes
aerobicyes78.769yes
halophileno93.586no
spore-formingno95.894no
glucose-fermentno92.349no
thermophileno98.3no
glucose-utilyes70.989yes

External links

@ref: 1444

culture collection no.: DSM 3660, IAM 14308, NCMB 1947, JCM 8519, ATCC 49418, CCM 3594, CCUG 35200, CIP 103534, IFO 15942, LMG 13179, NBRC 100250, NBRC 15942, NCIMB 1947

straininfo link

  • @ref: 75012
  • straininfo: 92568

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2764577Phenotypic and genomic studies of "Cytophaga psychrophila" isolated from diseased rainbow trout (Oncorhynchus mykiss) in France.Bernardet JF, Kerouault BAppl Environ Microbiol10.1128/aem.55.7.1796-1800.19891989Animals, Bacterial Infections/microbiology/*veterinary, Base Composition, Cytophaga/*classification/genetics/growth & development/metabolism, DNA, Bacterial/*analysis, Fish Diseases/*microbiology, France, Genotype, Nucleic Acid Hybridization, Phenotype, Salmonidae/*microbiology, Sequence Homology, Nucleic Acid, Trout/*microbiologyGenetics
Metabolism16119889Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance.Soule M, LaFrentz S, Cain K, LaPatra S, Call DRDis Aquat Organ10.3354/dao0652092005Base Sequence, Cloning, Molecular, Drug Resistance/*genetics, Elastin/*metabolism, Flavobacterium/*genetics/metabolism, Hydrolysis, Microarray Analysis, Molecular Sequence Data, *Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/*genetics, Sequence Alignment, Sequence Analysis, DNA, Tetracycline/*metabolismPhylogeny
Enzymology17425262Identification of potential vaccine target antigens by immunoproteomic analysis of a virulent and a non-virulent strain of the fish pathogen Flavobacterium psychrophilum.Sudheesh PS, LaFrentz BR, Call DR, Siems WF, LaPatra SE, Wiens GD, Cain KDDis Aquat Organ10.3354/dao0740372007Animals, Antigens, Bacterial/*analysis, Bacterial Proteins/genetics, Blotting, Western, Chaperonin 60/genetics, Chromatography, Liquid, Electrophoresis, Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Flavobacterium/genetics/immunology/*pathogenicity, Gene Expression/physiology, Immune Sera/metabolism, Immunoproteins/*analysis/isolation & purification, Molecular Sequence Data, Proteomics/methods, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Tandem Mass Spectrometry, VirulenceGenetics
Enzymology17498178Molecular typing by pulsed-field gel electrophoresis of Flavobacterium psychrophilum isolates derived from Japanese fish.Arai H, Morita Y, Izumi S, Katagiri T, Kimura HJ Fish Dis10.1111/j.1365-2761.2007.00809.x2007Animals, Cluster Analysis, Deoxyribonucleases, Type II Site-Specific/metabolism, Electrophoresis, Gel, Pulsed-Field/*veterinary, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Flavobacterium/classification/*genetics/isolation & purification, Genotype, Geography, Japan, Osmeriformes/*microbiology, Phylogeny, Polymerase Chain Reaction/veterinary, Polymorphism, Restriction Fragment LengthPhylogeny
Phylogeny19622646Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet.Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.008771-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/chemistry/classification/genetics/*isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Pathogenicity21488905Effect of biofilm formation on antimicrobial tolerance of Flavobacterium psychrophilum.Sundell K, Wiklund TJ Fish Dis10.1111/j.1365-2761.2011.01250.x2011Animals, Anti-Bacterial Agents/administration & dosage/*pharmacology, *Biofilms, Dose-Response Relationship, Drug, Drug Resistance, Bacterial/*physiology, Flavobacterium/*drug effects/physiology, Fluoroquinolones/administration & dosage/*pharmacology, Microbial Sensitivity Tests/veterinary, Oxytetracycline/administration & dosage/*pharmacology, Salmonidae/*microbiology
Genetics25685258Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).Wu AK, Kropinski AM, Lumsden JS, Dixon B, MacInnes JIStand Genomic Sci10.1186/1944-3277-10-32015
Phenotype28361040Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State.Levipan HA, Avendano-Herrera RFront Cell Infect Microbiol10.3389/fcimb.2017.000762017Biofilms/*growth & development, Flavobacterium/genetics/growth & development/*physiology, Gene Expression Profiling, Phenotype, Virulence
Stress29410654Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm.Levipan HA, Quezada J, Avendano-Herrera RFront Microbiol10.3389/fmicb.2018.000182018
Pathogenicity33824380Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum.Takeuchi M, Fujiwara-Nagata E, Katayama T, Suetake HSci Rep10.1038/s41598-021-87167-12021Animals, Aquaculture/methods, Fish Diseases/microbiology/*therapy, Flavobacteriaceae Infections/microbiology/therapy, Flavobacterium/*drug effects/genetics/pathogenicity, Oncorhynchus mykiss/genetics/*microbiology, Skin/microbiology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1444Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3660)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3660
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
41925Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15342
4334810.1007/978-0-387-68572-4
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/
68382Automatically annotated from API zym
75012Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92568.1StrainInfo: A central database for resolving microbial strain identifiers
122026Curators of the CIPCollection of Institut Pasteur (CIP 103534)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103534