Strain identifier

BacDive ID: 5545

Type strain: Yes

Species: Flavobacterium suncheonense

Strain Designation: GH 29-5, GH29-5

Strain history: CIP <- 2008, DSMZ <- KACC <- B.Y. Kim, RDA, Suwon, Korea: strain GH29-5

NCBI tax ID(s): 1121899 (strain), 350894 (species)

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General

@ref: 7150

BacDive-ID: 5545

DSM-Number: 17707

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

description: Flavobacterium suncheonense GH 29-5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil.

NCBI tax id

NCBI tax idMatching level
1121899strain
350894species

strain history

@refhistory
7150<- S. W. Kwon, KACC; GH 29-5 <- B.-Y. Kim et al.
123387CIP <- 2008, DSMZ <- KACC <- B.Y. Kim, RDA, Suwon, Korea: strain GH29-5

doi: 10.13145/bacdive5545.20230509.8.1

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

@ref: 7150

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium suncheonense

full scientific name: Flavobacterium suncheonense Kim et al. 2006 emend. Dong et al. 2013 emend. Tashkandy et al. 2016

strain designation: GH 29-5, GH29-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31773negative1.5-2.5 µm0.3 µmrod-shapedno
69480negative99.999
123387negativerod-shapedno

pigmentation

  • @ref: 31773
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17707_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17707_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17707_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17707_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17707_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7150R2A 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
42251MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123387CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7150positivegrowth28mesophilic
31773positivegrowth15-37
31773positiveoptimum30-37mesophilic
42251positivegrowth30mesophilic

culture pH

@refabilitytypepH
31773positivegrowth06-08
31773positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31773aerobe
123387obligate aerobe

spore formation

@refspore formationconfidence
31773no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31773NaClpositivegrowth0-1 %
31773NaClpositiveoptimum0-1 %

observation

  • @ref: 31773
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12338717632nitrate-reduction
12338716301nitrite-reduction

metabolite production

  • @ref: 123387
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31773catalase+1.11.1.6
31773gelatinase+
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
123387oxidase+
123387catalase+1.11.1.6
123387urease-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
123387-+++-++-+-++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7150greenhouse soilSuncheon cityRepublic of KoreaKORAsia
123387Environment, Greenhouse soilSuncheonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2316.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1250;97_1483;98_1808;99_2316&stattab=map
  • Last taxonomy: Flavobacterium suncheonense
  • 16S sequence: DQ222428
  • Sequence Identity:
  • Total samples: 2710
  • soil counts: 949
  • aquatic counts: 1259
  • animal counts: 410
  • plant counts: 92

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71501Risk group (German classification)
1233871Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7150
  • description: Flavobacterium suncheonense strain GH29-5 16S ribosomal RNA gene, partial sequence
  • accession: DQ222428
  • length: 1442
  • database: ena
  • NCBI tax ID: 350894

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium suncheonense GH29-5 = DSM 17707GCA_000430025scaffoldncbi1121899
66792Flavobacterium suncheonense GH29-5 = DSM 17707GCA_000769835contigncbi1121899
66792Flavobacterium suncheonense DSM 177071121899.3wgspatric1121899
66792Flavobacterium suncheonense GH29-5 = DSM 177071121899.5wgspatric1121899
66792Flavobacterium suncheonense GH29-5, DSM 177072524614632draftimg1121899
66792Flavobacterium suncheonense GH29-5, DSM 177072630968897draftimg1121899

GC content

@refGC-content
715039.0
3177339

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.016no
flagellatedno96.613yes
gram-positiveno98.925yes
anaerobicno99.184no
aerobicyes89.51no
halophileno96.559yes
spore-formingno95.539no
thermophileno97.754yes
glucose-utilyes78.135no
glucose-fermentno93.644no

External links

@ref: 7150

culture collection no.: DSM 17707, CIP 109901, KACC 11423

straininfo link

  • @ref: 75028
  • straininfo: 297213

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
Genetics27313837High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).Tashkandy N, Sabban S, Fakieh M, Meier-Kolthoff JP, Huang S, Tindall BJ, Rohde M, Baeshen MN, Baeshen NA, Lapidus A, Copeland A, Pillay M, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Goker M, Klenk HP, Kyrpides NC, Hahnke RLStand Genomic Sci10.1186/s40793-016-0159-52016

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7150Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17707)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17707
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
42251Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7697
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
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
75028Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297213.1StrainInfo: A central database for resolving microbial strain identifiers
123387Curators of the CIPCollection of Institut Pasteur (CIP 109901)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109901