Strain identifier

BacDive ID: 5546

Type strain: Yes

Species: Flavobacterium daejeonense

Strain Designation: GH1-10

Strain history: CIP <- 2008, DSMZ <- KACC <- B.Y. Kim, RDA, Suwon, Korea: strain GH1-10

NCBI tax ID(s): 1121887 (strain), 350893 (species)

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General

@ref: 7151

BacDive-ID: 5546

DSM-Number: 17708

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

description: Flavobacterium daejeonense GH1-10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil.

NCBI tax id

NCBI tax idMatching level
350893species
1121887strain

strain history

@refhistory
7151<- S. W. Kwon, KACC; GH1-10 <- B.-Y. Kim et al.
403392010, KACC
118842CIP <- 2008, DSMZ <- KACC <- B.Y. Kim, RDA, Suwon, Korea: strain GH1-10

doi: 10.13145/bacdive5546.20230509.8.1

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 daejeonense
  • full scientific name: Flavobacterium daejeonense Kim et al. 2006

@ref: 7151

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium daejeonense

full scientific name: Flavobacterium daejeonense Kim et al. 2006

strain designation: GH1-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31773negative02-03 µm0.5 µmrod-shapedno
118842negativerod-shapedno

pigmentation

  • @ref: 31773
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7151R2A 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
40339MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
42259MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118842CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7151positivegrowth28mesophilic
31773positivegrowth05-35
31773positiveoptimum30-35mesophilic
40339positivegrowth30mesophilic
42259positivegrowth30mesophilic

culture pH

@refabilitytypepH
31773positivegrowth06-08
31773positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31773aerobe
118842obligate aerobe

spore formation

  • @ref: 31773
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31773NaClpositivegrowth0-3 %
31773NaClpositiveoptimum0-3 %

observation

  • @ref: 31773
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3177322599arabinose+carbon source
3177317234glucose+carbon source
3177317306maltose+carbon source
3177337684mannose+carbon source
317734853esculin+hydrolysis
3177317632nitrate+reduction
11884217632nitrate+reduction
11884216301nitrite-reduction

metabolite production

  • @ref: 118842
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31773catalase+1.11.1.6
31773cytochrome 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
118842oxidase+
118842catalase+1.11.1.6
118842urease-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
118842-+++-++---++++-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7151greenhouse soilDaejeonRepublic of KoreaKORAsia
118842Environment, Greenhouse soilDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7707.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2832;97_4402;98_5636;99_7707&stattab=map
  • Last taxonomy: Flavobacterium daejeonense subclade
  • 16S sequence: DQ222427
  • Sequence Identity:
  • Total samples: 91
  • soil counts: 19
  • aquatic counts: 64
  • animal counts: 7
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71511Risk group (German classification)
1188421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7151
  • description: Flavobacterium daejeonense strain GH1-10 16S ribosomal RNA gene, partial sequence
  • accession: DQ222427
  • length: 1443
  • database: ena
  • NCBI tax ID: 350893

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium daejeonense DSM 17708GCA_000425425scaffoldncbi1121887
66792Flavobacterium daejeonense DSM 177081121887.3wgspatric1121887
66792Flavobacterium daejeonense DSM 177082523533615draftimg1121887

GC content

@refGC-content
715135.0
3177335

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.422yes
flagellatedno94.029yes
gram-positiveno98.465yes
anaerobicno99.643yes
aerobicyes86.521no
halophileno97.059no
spore-formingno94.879yes
thermophileno97.565no
glucose-utilyes86.724yes
glucose-fermentno88.753no

External links

@ref: 7151

culture collection no.: DSM 17708, CIP 109900, KACC 11422, CIP 110192

straininfo link

  • @ref: 75029
  • straininfo: 297197

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825643Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea.Kim BY, Weon HY, Cousin S, Yoo SH, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64243-02006Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flavobacterium/*classification/cytology/*isolation & purification/physiology, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Phenazines, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysis/chemistryGenetics
Phylogeny27902211Flavobacterium eburneum sp. nov., isolated from reclaimed saline land soil.Hwang WM, Kim D, Kang K, Ahn TYInt J Syst Evol Microbiol10.1099/ijsem.0.0015682017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32629361Flavobacterium pokkalii sp. nov., a novel plant growth promoting native rhizobacteria isolated from pokkali rice grown in coastal saline affected agricultural regions of southern India, Kerala.Menon RR, Kumari S, Viver T, Rameshkumar NMicrobiol Res10.1016/j.micres.2020.1265332020DNA, Bacterial/genetics, Flavobacterium/classification/genetics/*isolation & purification/*physiology, India, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oryza/*growth & development/*microbiology, Phylogeny, *Plant Development, RNA, Ribosomal, 16S/genetics, Rhizosphere, Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7151Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17708)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17708
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
31773Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2804628776041
40339Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8024
42259Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7696
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
75029Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297197.1StrainInfo: A central database for resolving microbial strain identifiers
118842Curators of the CIPCollection of Institut Pasteur (CIP 109900)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109900