Strain identifier

BacDive ID: 5549

Type strain: Yes

Species: Flavobacterium terrigena

Strain Designation: DS-20

Strain history: CIP <- 2009, DSMZ <- J.H. Yoon, KRIBB, Taejon, Korea: strain DS-20

NCBI tax ID(s): 402734 (species)

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General

@ref: 7175

BacDive-ID: 5549

DSM-Number: 17934

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

description: Flavobacterium terrigena DS-20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 402734
  • Matching level: species

strain history

@refhistory
7175<- J.-H. Yoon, KRIBB; DS-20
67771<- JH Yoon, KRIBB
123476CIP <- 2009, DSMZ <- J.H. Yoon, KRIBB, Taejon, Korea: strain DS-20

doi: 10.13145/bacdive5549.20230509.8.1

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 terrigena
  • full scientific name: Flavobacterium terrigena Yoon et al. 2007

@ref: 7175

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium terrigena

full scientific name: Flavobacterium terrigena Yoon et al. 2007 emend. Fujii et al. 2014 emend. Hahnke et al. 2016

strain designation: DS-20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31993negative1.6 µm0.45 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.998
123476negativerod-shapedno

pigmentation

  • @ref: 31993
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7175R2A 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
33340MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123476CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123476CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
123476CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7175positivegrowth25mesophilic
31993positivegrowth10-30
31993positiveoptimum25mesophilic
33340positivegrowth30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
31993positivegrowth06-08
31993positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31993aerobe
67771aerobe
123476obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31993286442-oxopentanoate+carbon source
319935291gelatin+carbon source
3199329987glutamate+carbon source
3199318257ornithine+carbon source
3199326271proline+carbon source
3199351850methyl pyruvate+carbon source
3199317822serine+carbon source
3199330031succinate+carbon source
3199326986threonine+carbon source
3199353424tween 20+carbon source
3199353423tween 40+carbon source
3199353425tween 60+carbon source
3199353426tween 80+carbon source
12347617632nitrate-reduction
12347616301nitrite-reduction

metabolite production

  • @ref: 123476
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31993alkaline phosphatase+3.1.3.1
31993catalase+1.11.1.6
31993gelatinase+
31993cytochrome 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
123476oxidase+
123476catalase+1.11.1.6
123476urease+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
123476-+-+-++---++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7175soilDokdoRepublic of KoreaKORAsia
67771From soilDokdoRepublic of KoreaKORAsia
123476Environment, SoilDokdo IslandRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_74982.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_13281;97_16147;98_23462;99_74982&stattab=map
  • Last taxonomy: Flavobacterium terrigena subclade
  • 16S sequence: DQ889724
  • Sequence Identity:
  • Total samples: 1426
  • soil counts: 62
  • aquatic counts: 1062
  • animal counts: 183
  • plant counts: 119

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71751Risk group (German classification)
1234761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7175
  • description: Flavobacterium terrigena strain DS-20 16S ribosomal RNA gene, partial sequence
  • accession: DQ889724
  • length: 1470
  • database: ena
  • NCBI tax ID: 402734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium terrigena DSM 17934GCA_900108955scaffoldncbi402734
66792Flavobacterium terrigena strain DSM 17934402734.4wgspatric402734
66792Flavobacterium terrigena DSM 179342600255390draftimg402734

GC content

@refGC-contentmethod
717538.2high performance liquid chromatography (HPLC)
3199338.2
717531.2sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno93.316no
motileno91.877yes
flagellatedno95.417no
gram-positiveno99.012yes
anaerobicno99.1yes
aerobicyes89.72yes
halophileno97.026no
spore-formingno95.477no
thermophileno99.174yes
glucose-utilyes77.467no

External links

@ref: 7175

culture collection no.: DSM 17934, CIP 109939, KCTC 12761

straininfo link

  • @ref: 75031
  • straininfo: 308609

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473238Flavobacterium terrigena sp. nov., isolated from soil.Yoon JH, Kang SJ, Lee JS, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64776-02007Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/growth & development/*isolation & purification, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny20601490Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond.Sheu SY, Chiu TF, Young CC, Arun AB, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.025403-02010Aerobiosis, Animals, Aquaculture, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Fresh Water, Hydrogen-Ion Concentration, Molecular Sequence Data, Palaemonidae/*microbiology, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan, TemperatureGenetics
Phylogeny34136928Flavobacterium difficile sp. nov., isolated from a freshwater waterfall.Chen WM, You YX, Young CC, Lin SY, Sheu SYArch Microbiol10.1007/s00203-021-02440-12021Fatty Acids, *Flavobacterium/classification/genetics, *Fresh Water/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Taiwan

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7175Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17934)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17934
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
31993Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824728776041
33340Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7739
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75031Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308609.1StrainInfo: A central database for resolving microbial strain identifiers
123476Curators of the CIPCollection of Institut Pasteur (CIP 109939)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109939