Strain identifier

BacDive ID: 5565

Type strain: Yes

Species: Flavobacterium cucumis

Strain Designation: R2A45-3

Strain history: CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830

NCBI tax ID(s): 416016 (species)

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

@ref: 7727

BacDive-ID: 5565

DSM-Number: 18830

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

description: Flavobacterium cucumis R2A45-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil cultivated with cucumber.

NCBI tax id

  • NCBI tax id: 416016
  • Matching level: species

strain history

@refhistory
7727<- S.-W. Kwon, KACC; R2A45-3 <- H.-Y. Weon et al., Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea
118807CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830

doi: 10.13145/bacdive5565.20230509.8.1

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 cucumis
  • full scientific name: Flavobacterium cucumis Weon et al. 2007

@ref: 7727

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium cucumis

full scientific name: Flavobacterium cucumis Weon et al. 2007

strain designation: R2A45-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32083negative2.5 µm0.5 µmrod-shapedyesgliding
69480negative99.998
118807negativerod-shapedno

pigmentation

  • @ref: 32083
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7727R2A 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
33335MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118807CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7727positivegrowth30mesophilic
32083positivegrowth05-37
32083positiveoptimum30mesophilic
33335positivegrowth30mesophilic

culture pH

@refabilitytypepH
32083positivegrowth06-08
32083positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32083aerobe
118807obligate aerobe

spore formation

@refspore formationconfidence
32083no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
32083NaClpositivegrowth0-2 %
32083NaClpositiveoptimum0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
320834853esculin+hydrolysis
11880717632nitrate-reduction
11880716301nitrite-reduction

metabolite production

  • @ref: 118807
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32083acid phosphatase+3.1.3.2
32083alkaline phosphatase+3.1.3.1
32083alpha-galactosidase+3.2.1.22
32083catalase+1.11.1.6
32083cytochrome 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
118807oxidase+
118807catalase+1.11.1.6
118807urease-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
118807-+++-+++++++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7727greenhouse soil cultivated with cucumberSangju regionRepublic of KoreaKORAsia
118807Environment, Greenhouse soilsSuwonRepublic of KoreaKORAsia2007

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1103.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_644;97_747;98_866;99_1103&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: EF126993
  • Sequence Identity:
  • Total samples: 3245
  • soil counts: 257
  • aquatic counts: 2595
  • animal counts: 363
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77271Risk group (German classification)
1188071Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7727
  • description: Flavobacterium cucumis strain R2A45-3 16S ribosomal RNA gene, partial sequence
  • accession: EF126993
  • length: 1439
  • database: ena
  • NCBI tax ID: 416016

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium cucumis DSM 18830GCA_900148835contigncbi416016
66792Flavobacterium cucumis strain DSM 18830416016.4wgspatric416016
66792Flavobacterium cucumis DSM 188302698536819draftimg416016

GC content

@refGC-content
772738.0
3208338

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.916no
anaerobicno98.604yes
halophileno93.29no
spore-formingno95.501no
glucose-utilyes84.901no
aerobicyes85.83no
flagellatedno94.137yes
thermophileno98.247no
motileno89.818no
glucose-fermentno92.989no

External links

@ref: 7727

culture collection no.: DSM 18830, CIP 109888, KACC 11732

straininfo link

  • @ref: 75047
  • straininfo: 309451

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625200Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64935-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny18768627Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir.Qu JH, Li HF, Yang JS, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.65586-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny19406812Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals.Yoon HS, Aslam Z, Song GC, Kim SW, Jeon CO, Chon TS, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.004978-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Industrial Waste, Korea, *Metals, Heavy, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*chemistry/*microbiology, Sequence Analysis, DNA, Species Specificity, *Water Pollution, ChemicalGenetics
Phylogeny23543500Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field.Subhash Y, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.050047-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triterpenes/analysis, *Water Microbiology, beta Carotene/analysisGenetics
Phylogeny31758394Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil.Kim I, Kim J, Chhetri G, Seo TJ Microbiol10.1007/s12275-019-9350-x2019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/*metabolism, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Pigments, Biological/*metabolism, Polyenes/*metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisMetabolism
Phylogeny35059830Flavobacterium proteolyticum sp. nov., isolated from aquaculture water.Du J, Liu Y, Pei T, Li A, Deng MR, Zhu HArch Microbiol10.1007/s00203-021-02744-22022Aquaculture, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Flavobacterium/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *WaterTranscriptome
Phylogeny35731344Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead).Kang S, Lee JY, Han JE, Jeong YS, Gim DH, Bae JWJ Microbiol10.1007/s12275-022-2075-22022Animals, Bacterial Typing Techniques, Bivalvia, Cordyceps, DNA, Bacterial/genetics, *Fatty Acids/analysis, Fishes, *Flavobacterium, Intestines, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7727Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18830)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18830
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
32083Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2832928776041
33335Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7683
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
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
75047Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309451.1StrainInfo: A central database for resolving microbial strain identifiers
118807Curators of the CIPCollection of Institut Pasteur (CIP 109888)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109888