Strain identifier

BacDive ID: 5575

Type strain: Yes

Species: Flavobacterium rivuli

Strain Designation: WB3.3-2

Strain history: CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB 3.3-2

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 15951

BacDive-ID: 5575

DSM-Number: 21788

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

description: Flavobacterium rivuli WB3.3-2 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from water of a hardwater creek.

NCBI tax id

NCBI tax idMatching level
498301species
1121895strain

strain history

@refhistory
15951<- Z. Ali, DSMZ; WB3.3-2 <- E. Brambilla and O. Päuker, DSMZ
122243CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB 3.3-2

doi: 10.13145/bacdive5575.20230509.8.1

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

@ref: 15951

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium rivuli

full scientific name: Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013

strain designation: WB3.3-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29215negative2 µm0.5 µmrod-shapedno
69480negative99.998
122243negativerod-shapedno

colony morphology

  • @ref: 61780
  • incubation period: 1-2 days

pigmentation

  • @ref: 29215
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21788_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21788_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21788_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21788_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21788_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21788_6.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15951R2A 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
42068MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122243CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15951positivegrowth20psychrophilic
29215positivegrowth04-29
29215positiveoptimum16-24psychrophilic
42068positivegrowth25mesophilic
61780positivegrowth30mesophilic

culture pH

@refabilitytypepH
29215positivegrowth6.4-7.8
29215positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29215aerobe
61780aerobe
122243obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
29215NaClpositivegrowth0-2 %
29215NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2921530089acetate+carbon source
2921522599arabinose+carbon source
2921517057cellobiose+carbon source
2921528757fructose+carbon source
2921528260galactose+carbon source
2921517234glucose+carbon source
2921517716lactose+carbon source
2921517306maltose+carbon source
2921537684mannose+carbon source
2921528053melibiose+carbon source
2921551850methyl pyruvate+carbon source
2921526271proline+carbon source
2921526986threonine+carbon source
2921527082trehalose+carbon source
2921553423tween 40+carbon source
292154853esculin+hydrolysis
12224317632nitrate-reduction
12224316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2921516136hydrogen sulfideyes
12224335581indoleno

enzymes

@refvalueactivityec
29215catalase+1.11.1.6
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
122243oxidase+
122243catalase+1.11.1.6
122243urease-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
122243-+-+-++---++++------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15951water of a hardwater creekHarz Mountains, Westerhöfer Bach, Westerhof, 40 km north of GöttingenGermanyDEUEurope
61780Water,hardwater creekWesterhof,Harz MountainsGermanyDEUEurope
122243Environment, Hard water, riverWesterhöfer Bach, Harz mountainsGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2658.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1182;97_1690;98_2058;99_2658&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: AM934661
  • Sequence Identity:
  • Total samples: 3441
  • soil counts: 370
  • aquatic counts: 1682
  • animal counts: 1194
  • plant counts: 195

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159511Risk group (German classification)
1222431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15951
  • description: Flavobacterium rivuli partial 16S rRNA gene, type strain WB3.3-2T
  • accession: AM934661
  • length: 1488
  • database: ena
  • NCBI tax ID: 498301

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium rivuli WB 3.3-2 = DSM 21788GCA_000378485scaffoldncbi1121895
66792Flavobacterium rivuli WB 3.3-2 = DSM 21788GCA_000769825contigncbi1121895
66792Flavobacterium rivuli DSM 217881121895.5wgspatric1121895
66792Flavobacterium rivuli WB 3.3-2 = DSM 217881121895.7wgspatric1121895
66792Flavobacterium rivuli DSM 217882519103183draftimg1121895

GC content

@refGC-contentmethod
1595140.4high performance liquid chromatography (HPLC)
2921540.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.448no
flagellatedno96.452yes
gram-positiveno98.303no
anaerobicno99.449yes
aerobicyes90.722no
halophileno92.741yes
spore-formingno95.139no
thermophileno99.202no
glucose-utilyes86.619yes
glucose-fermentno91.709no

External links

@ref: 15951

culture collection no.: DSM 21788, CIP 109865, CCUG 58934, WB 3.3-2

straininfo link

  • @ref: 75057
  • straininfo: 363443

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
Genetics26380634High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HPStand Genomic Sci10.1186/s40793-015-0032-y2015Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15951Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21788)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21788
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
42068Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7658
61780Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58934)https://www.ccug.se/strain?id=58934
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
75057Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363443.1StrainInfo: A central database for resolving microbial strain identifiers
122243Curators of the CIPCollection of Institut Pasteur (CIP 109865)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109865