Strain identifier

BacDive ID: 5568

Type strain: Yes

Species: Flavobacterium hercynium

Strain Designation: WB4.2-33

Strain history: CIP <- 2006, DSMZ <- O. Päuker: strain WB 4.2-33

NCBI tax ID(s): 387094 (species)

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General

@ref: 7488

BacDive-ID: 5568

DSM-Number: 18292

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

description: Flavobacterium hercynium WB4.2-33 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 387094
  • Matching level: species

strain history

@refhistory
7488<- S. Cousin <- O. Päuker; WB4.2-33
119882CIP <- 2006, DSMZ <- O. Päuker: strain WB 4.2-33

doi: 10.13145/bacdive5568.20230509.8.1

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 hercynium
  • full scientific name: Flavobacterium hercynium Cousin et al. 2007

@ref: 7488

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium hercynium

full scientific name: Flavobacterium hercynium Cousin et al. 2007 emend. Kim et al. 2012

strain designation: WB4.2-33

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31865negative5.8-6.3 µm0.7-0.8 µmrod-shapedyesgliding
69480negative99.995
119882negativerod-shapedno

pigmentation

  • @ref: 31865
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7488R2A 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
42257MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119882CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7488positivegrowth25mesophilic
31865positivegrowth12-29
31865positiveoptimum23.5psychrophilic
42257positivegrowth25mesophilic

culture pH

@refabilitytypepH
31865positivegrowth6.0-8.0
31865positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31865aerobe
119882obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
31865NaClpositivegrowth0-1 %
31865NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3186540585alpha-cyclodextrin+carbon source
3186518403L-arabitol+carbon source
3186522653asparagine+carbon source
3186535391aspartate+carbon source
3186517057cellobiose+carbon source
3186516947citrate+carbon source
3186528757fructose+carbon source
3186528260galactose+carbon source
3186528087glycogen+carbon source
3186517306maltose+carbon source
3186529864mannitol+carbon source
3186537684mannose+carbon source
3186537657methyl D-glucoside+carbon source
31865506227N-acetylglucosamine+carbon source
3186518257ornithine+carbon source
3186526986threonine+carbon source
3186527082trehalose+carbon source
3186553258sodium citrate+carbon source
318654853esculin+hydrolysis
3186517632nitrate+reduction
11988217632nitrate+reduction
11988216301nitrite+reduction

metabolite production

  • @ref: 119882
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31865acid phosphatase+3.1.3.2
31865alkaline phosphatase+3.1.3.1
31865catalase+1.11.1.6
31865gelatinase+
31865cytochrome oxidase+1.9.3.1
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
119882oxidase+
119882alcohol dehydrogenase-1.1.1.1
119882catalase+1.11.1.6
119882lysine decarboxylase-4.1.1.18
119882ornithine decarboxylase-4.1.1.17
119882urease-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
119882-+++-++---++-+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7488stream waterLower Saxony, Westhöfer BachGermanyDEUEurope
119882Environment, Hard water creekGermanyDEUEurope2005

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74881Risk group (German classification)
1198821Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium hercynium strain DSM 18292 16S ribosomal RNA gene, partial sequenceJX6570421223ena387094
7488Flavobacterium hercynium partial 16S rRNA gene, type strain WB 4.2-33TAM2656231502ena387094

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium hercynium DSM 18292GCA_002217285scaffoldncbi387094
66792Flavobacterium hercynium strain DSM 18292387094.4wgspatric387094
66792Flavobacterium hercynium DSM 182922724679814draftimg387094

GC content

@refGC-contentmethod
748833.9fluorimetric
3186537.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.121yes
gram-positiveno98.097no
anaerobicno99.62no
aerobicyes90.3no
halophileno95.429yes
spore-formingno92.759no
thermophileno99.587no
glucose-utilyes87.293no
motileno83.018no
glucose-fermentno86.521no

External links

@ref: 7488

culture collection no.: DSM 18292, LMG 26768, CIP 109241, WB 4.2-33

straininfo link

  • @ref: 75051
  • straininfo: 297201

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267958Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek.Cousin S, Pauker O, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64556-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flavobacterium/*classification/cytology/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Water MicrobiologyGenetics
Phylogeny19542120Flavobacterium chungangense sp. nov., isolated from a freshwater lake.Kim JH, Kim KY, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.007955-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7488Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18292
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
31865Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128125
42257Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6960
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)
68382Automatically annotated from API zym
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
75051Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297201.1StrainInfo: A central database for resolving microbial strain identifiers
119882Curators of the CIPCollection of Institut Pasteur (CIP 109241)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109241