Strain identifier

BacDive ID: 5652

Type strain: Yes

Species: Tenacibaculum ovolyticum

Strain Designation: EKD 002

Strain history: CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- G.H. Hansen: strain EKD 002

NCBI tax ID(s): 1123347 (strain), 104270 (species)

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General

@ref: 7396

BacDive-ID: 5652

DSM-Number: 18103

keywords: genome sequence, 16S sequence, Bacteria, aerobe, motile, rod-shaped, animal pathogen

description: Tenacibaculum ovolyticum EKD 002 is an aerobe, motile, rod-shaped animal pathogen that was isolated from adherent epiflora of Atlantic Halibut eggs.

NCBI tax id

NCBI tax idMatching level
104270species
1123347strain

strain history

@refhistory
7396<- NCIMB <- G. H. Hansen; EKD 002
67770IAM 14318 <-- NCIMB 13127 <-- G. H. Hansen EKD002.
121477CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- G.H. Hansen: strain EKD 002

doi: 10.13145/bacdive5652.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Tenacibaculum
  • species: Tenacibaculum ovolyticum
  • full scientific name: Tenacibaculum ovolyticum (Hansen et al. 1992) Suzuki et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Flexibacter ovolyticus

@ref: 7396

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Tenacibaculum

species: Tenacibaculum ovolyticum

full scientific name: Tenacibaculum ovolyticum (Hansen et al. 1992) Suzuki et al. 2001

strain designation: EKD 002

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityflagellum arrangementgram stainconfidence
433752-20 µm0.5 µmrod-shapedyesgliding
121477rod-shapednonegative
69480negative96
69480no90

colony morphology

  • @ref: 43375
  • colony color: pale yellow

pigmentation

  • @ref: 121477
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7396BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
39511Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121477CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7396positivegrowth15
39511positivegrowth15
43375positivegrowth4-25
52587positivegrowth15
67770positivegrowth15
121477positivegrowth5-25
121477nogrowth30

culture pH

  • @ref: 43375
  • ability: positive
  • type: growth
  • pH: 5.9-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 52587
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43375309162-oxoglutarate-growth
4337530089acetate-growth
433752509agar-degradation
4337535391aspartate-growth
4337516150benzoate-growth
43375casamino acids+growth
43375casamino acids+/-growth
43375casein+degradation
4337562968cellulose-degradation
4337517029chitin+degradation
4337516947citrate-growth
4337516988D-ribose-growth
4337525115malate-growth
4337516991dna+degradation
433754853esculin-degradation
4337516236ethanol-growth
4337529806fumarate-growth
433755291gelatin+degradation
4337517754glycerol-growth
4337529985L-glutamate-growth
4337515603L-leucine-growth
4337517203L-proline-growth
4337530924L-tartrate-growth
4337517790methanol-growth
43375506227N-acetylglucosamine-growth
4337517632nitrate+reduction
4337517272propionate-growth
4337515361pyruvate-growth
4337528017starch-degradation
4337530031succinate-growth
4337517992sucrose-growth
43375tryptone+growth
4337553426tween 80+degradation
4337518186tyrosine+degradation
1214774853esculin-hydrolysis
121477606565hippurate-hydrolysis
12147717632nitrate+reduction
12147716301nitrite-reduction

metabolite production

  • @ref: 121477
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43375cytochrome oxidase+1.9.3.1
43375catalase+1.11.1.6
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
121477oxidase+
121477beta-galactosidase-3.2.1.23
121477alcohol dehydrogenase-1.1.1.1
121477gelatinase+
121477amylase-
121477caseinase+3.4.21.50
121477catalase-1.11.1.6
121477tween esterase+
121477gamma-glutamyltransferase+2.3.2.2
121477lecithinase-
121477lipase-
121477lysine decarboxylase-4.1.1.18
121477ornithine decarboxylase-4.1.1.17
121477phenylalanine ammonia-lyase-4.3.1.24
121477protease+
121477tryptophan deaminase-
121477urease-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
121477-+++-+++--++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesisolation date
7396adherent epiflora of Atlantic Halibut (Hippoglossus hippoglossus L) eggsNorwayNOREurope
52587Halibut,adherent epiflora of Atlantic halibut eggs
67770Adherent epiflora of Atlantic halibut (Hippoglossus hippoglossus) eggsNorwayNOREuropeHippoglossus hippoglossus
121477Atlantic halibut, Hippoglossus hipoglossus, eggsNorwayNOREurope1989

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body Product#Urogenital tract#Egg

taxonmaps

  • @ref: 69479
  • File name: preview.99_1874.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_1052;97_1229;98_1476;99_1874&stattab=map
  • Last taxonomy: Tenacibaculum ovolyticum subclade
  • 16S sequence: AB032506
  • Sequence Identity:
  • Total samples: 1310
  • soil counts: 22
  • aquatic counts: 1136
  • animal counts: 152

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7396yes1Risk group (German classification)
1214771Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tenacibaculum ovolyticus gene for 16S rRNA, partial sequence, strain:IAM14318AB0325061440nuccore104270
7396Tenacibaculum ovolyticum gene for 16S rRNA, strain:IFO 15947AB0780581473nuccore104270
124043Tenacibaculum ovolyticum gene for 16S rRNA, partial sequence, strain: NBRC 15947.AB6810051443nuccore104270

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tenacibaculum ovolyticum DSM 181031123347.4wgspatric1123347
66792Tenacibaculum ovolyticum DSM 181032523533531draftimg1123347
67770Tenacibaculum ovolyticum DSM 18103GCA_000430545scaffoldncbi1123347

GC content

  • @ref: 43375
  • GC-content: 30.3-32

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno96no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.849yes
69480spore-formingspore-formingAbility to form endo- or exosporesno85.2no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.505yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.972yes
69480flagellatedmotile2+Ability to perform flagellated movementno90yes

External links

@ref: 7396

culture collection no.: CCUG 35199, CIP 106403, DSM 18103, ATCC 51887, IAM 14318, IFO 15947, NCIMB 13127, JCM 21158, LMG 13026, NBRC 15947

straininfo link

  • @ref: 75135
  • straininfo: 13990

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1503974Flexibacter ovolyticus sp. nov., a pathogen of eggs and larvae of Atlantic halibut, Hippoglossus hippoglossus L.Hansen GH, Bergh O, Michaelsen J, Knappskog DInt J Syst Bacteriol10.1099/00207713-42-3-4511992Animals, Bacterial Proteins/chemistry, Bacteroidetes/*classification/isolation & purification/physiology/ultrastructure, DNA, Bacterial/chemistry, Electrophoresis, Polyacrylamide Gel, Fishes/*microbiology, Microscopy, Electron, Nucleic Acid Hybridization, Ovum/microbiology, PhenotypeEnzymology
Phylogeny26662517Tenacibaculum finnmarkense sp. nov., a fish pathogenic bacterium of the family Flavobacteriaceae isolated from Atlantic salmon.Smage SB, Brevik OJ, Duesund H, Ottem KF, Watanabe K, Nylund AAntonie Van Leeuwenhoek10.1007/s10482-015-0630-02015Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Molecular Sequence Data, Norway, Phylogeny, RNA, Ribosomal, 16S/genetics, Salmo salar/*microbiology, Tenacibaculum/classification/genetics/*isolation & purification/metabolismMetabolism
Genetics27365358Genome Sequence of the Psychrophilic Bacterium Tenacibaculum ovolyticum Strain da5A-8 Isolated from Deep Seawater.Teramoto M, Zhai Z, Komatsu A, Shibayama K, Suzuki MGenome Announc10.1128/genomeA.00644-162016Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7396Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18103)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18103
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
39511Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18529
43375Makoto Suzuki, Yasuyoshi Nakagawa, Shigeaki Harayama, Satoshi Yamamoto10.1099/00207713-51-5-1639Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria : proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov.IJSEM 51: 1639-1652 200111594591
52587Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35199)https://www.ccug.se/strain?id=35199
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
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75135Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13990.1StrainInfo: A central database for resolving microbial strain identifiers
121477Curators of the CIPCollection of Institut Pasteur (CIP 106403)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106403
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy