Strain identifier

BacDive ID: 5576

Type strain: Yes

Species: Flavobacterium subsaxonicum

Strain Designation: WB4.1-42

Strain history: CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB4.1-42

NCBI tax ID(s): 1121898 (strain), 426226 (species)

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General

@ref: 15953

BacDive-ID: 5576

DSM-Number: 21790

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

description: Flavobacterium subsaxonicum WB4.1-42 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from water of a hardwater creek.

NCBI tax id

NCBI tax idMatching level
426226species
1121898strain

strain history

@refhistory
15953<- Z. Ali, DSMZ; WB4.1-42 <- E. Brambilla and O. Päuker, DSMZ
123348CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB4.1-42

doi: 10.13145/bacdive5576.20230509.8.1

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 subsaxonicum
  • full scientific name: Flavobacterium subsaxonicum Ali et al. 2009

@ref: 15953

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium subsaxonicum

full scientific name: Flavobacterium subsaxonicum Ali et al. 2009 emend. Dong et al. 2013 emend. Hahnke et al. 2016

strain designation: WB4.1-42

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29215negative4 µm1.5 µmrod-shapedno
69480negative99.997
123348negativerod-shapedno

pigmentation

  • @ref: 29215
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15953R2A 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
37858MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123348CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15953positivegrowth24psychrophilic
29215positivegrowth02-38
29215positiveoptimum24-28
37858positivegrowth25mesophilic

culture pH

@refabilitytypepH
29215positivegrowth7.0-7.6
29215positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29215aerobe
123348obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 29215
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2921516449alanine+carbon source
2921522599arabinose+carbon source
2921517057cellobiose+carbon source
2921528757fructose+carbon source
2921533984fucose+carbon source
2921528260galactose+carbon source
2921517234glucose+carbon source
2921524996lactate+carbon source
2921517306maltose+carbon source
2921537684mannose+carbon source
2921528053melibiose+carbon source
2921537657methyl D-glucoside+carbon source
2921518257ornithine+carbon source
2921526271proline+carbon source
2921526546rhamnose+carbon source
2921517822serine+carbon source
2921526986threonine+carbon source
292154853esculin+hydrolysis
12334817632nitrate-reduction
12334816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2921516136hydrogen sulfideyes
12334835581indoleno

enzymes

@refvalueactivityec
29215catalase+1.11.1.6
29215gelatinase+
29215cytochrome 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
123348oxidase+
123348catalase+1.11.1.6
123348urease-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
123348-+-+-+++--+-++--+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15953water of a hardwater creekHarz Mountains, Westerhöfer Bach, Westerhof, 40 km north of GöttingenGermanyDEUEurope
123348Environment, Hard water, riverWesterhöfer Bach, Harz mountainsGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2161.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1182;97_1389;98_1687;99_2161&stattab=map
  • Last taxonomy: Flavobacterium subsaxonicum subclade
  • 16S sequence: AM934666
  • Sequence Identity:
  • Total samples: 709
  • soil counts: 110
  • aquatic counts: 412
  • animal counts: 109
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159531Risk group (German classification)
1233481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15953
  • description: Flavobacterium subsaxonicum partial 16S rRNA gene, type strain WB4.1-42T
  • accession: AM934666
  • length: 1488
  • database: ena
  • NCBI tax ID: 426226

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium subsaxonicum WB 4.1-42 = DSM 21790GCA_000422725scaffoldncbi1121898
66792Flavobacterium subsaxonicum WB 4.1-42 = DSM 21790GCA_000769935contigncbi1121898
66792Flavobacterium subsaxonicum DSM 217901121898.3wgspatric1121898
66792Flavobacterium subsaxonicum WB 4.1-42 = DSM 217901121898.5wgspatric1121898
66792Flavobacterium subsaxonicum DSM 217902524614667draftimg1121898

GC content

@refGC-contentmethod
1595343.3high performance liquid chromatography (HPLC)
2921543.3
1595341.6sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.271no
flagellatedno95.412no
gram-positiveno98.214no
anaerobicno99.08no
aerobicyes87.206yes
halophileno94.916no
spore-formingno95.542no
thermophileno99.241yes
glucose-utilyes90.369yes
glucose-fermentno90.748no

External links

@ref: 15953

culture collection no.: DSM 21790, CIP 109867, WB 4.1-42

straininfo link

  • @ref: 75058
  • straininfo: 363444

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny23456809Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli.Dong K, Xu B, Zhu F, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.048652-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23475344Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium.Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SPInt J Syst Evol Microbiol10.1099/ijs.0.047217-02013Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Hawaii, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wikstroemia/*microbiology, Wood/*microbiology, Xanthophylls/analysis, ZeaxanthinsGenetics
Phylogeny31433290Flavobacterium cerinum sp. nov., isolated from Arctic tundra soil.Zhang R, Zhang XY, Sun XK, Mu DS, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0036482019Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Tundra, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15953Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21790)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21790
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
29215Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2563628776041
37858Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7660
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
75058Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363444.1StrainInfo: A central database for resolving microbial strain identifiers
123348Curators of the CIPCollection of Institut Pasteur (CIP 109867)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109867