Strain identifier

BacDive ID: 134059

Type strain: Yes

Species: Flavobacterium ginsengisoli

Strain history: CIP <- 2014, JCM <- 2010, DC. Yang, Kyung Hee Univ., Gyeonggi-do, Korea: strain DCY54

NCBI tax ID(s): 871694 (species)

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General

@ref: 31154

BacDive-ID: 134059

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

description: Flavobacterium ginsengisoli KCTC 23318 is an aerobe, Gram-negative, motile bacterium that was isolated from Soil of a field cultivated with ginseng.

NCBI tax id

  • NCBI tax id: 871694
  • Matching level: species

strain history

@refhistory
67770D.-C. Yang DCY54.
67771<- YJ KIm, Kyunghee Univ.
119626CIP <- 2014, JCM <- 2010, DC. Yang, Kyung Hee Univ., Gyeonggi-do, Korea: strain DCY54

doi: 10.13145/bacdive134059.20250331.9.3

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 ginsengisoli
  • full scientific name: Flavobacterium ginsengisoli Kim et al. 2013

@ref: 31154

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium ginsengisoli

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31154negative3.85 µm0.75 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative
125438no91.1
125438negative93.293
119626negativerod-shapedno

pigmentation

  • @ref: 31154
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41606MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119626CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
31154positivegrowth04-35
31154positiveoptimum27.5
41606positivegrowth30
67770positivegrowth30
67771positivegrowth28

culture pH

@refabilitytypepHPH range
31154positivegrowth05-09alkaliphile
31154positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31154aerobe
67771aerobe

spore formation

  • @ref: 31154
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31154NaClpositivegrowth0-2 %
31154NaClpositiveoptimum0.5 %

observation

@refobservation
31154aggregates in clumps
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3115422599arabinose+carbon source
3115417234glucose+carbon source
3115417306maltose+carbon source
3115437684mannose+carbon source
31154506227N-acetylglucosamine+carbon source
311544853esculin+hydrolysis
3115417632nitrate+reduction

enzymes

@refvalueactivityec
31154acid phosphatase+3.1.3.2
31154alkaline phosphatase+3.1.3.1
31154alpha-galactosidase+3.2.1.22
31154catalase+1.11.1.6
31154gelatinase+
31154cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Soil of a field cultivated with ginsengYongin ProvinceRepublic of KoreaKORAsia
67771From soil of a field cultivated with ginsengYongin provinceRepublic of KoreaKORAsia
119626Environment, Soil of a field cultivated with ginsengYongin ProvinceRepublic of KoreaKORAsia

taxonmaps

  • @ref: 69479
  • File name: preview.99_159038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_207;97_5673;98_38607;99_159038&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: HM776705
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 15
  • aquatic counts: 12
  • animal counts: 2
  • plant counts: 1

Safety information

risk assessment

  • @ref: 119626
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31154
  • description: Flavobacterium ginsengisoli strain DCY54 16S ribosomal RNA gene, partial sequence
  • accession: HM776705
  • length: 1408
  • database: nuccore
  • NCBI tax ID: 871694

Genome sequences

  • @ref: 66792
  • description: Flavobacterium ginsengisoli KCTC 23318
  • accession: GCA_029625315
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 871694

GC content

  • @ref: 31154
  • GC-content: 33.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno93.293yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.814yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.603yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.469no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.54yes
125438motile2+flagellatedAbility to perform flagellated movementno91.1no

External links

@ref: 31154

culture collection no.: KCTC 23318, JCM 17336, DCY 54, BCRC 81040, CIP 110819

straininfo link

  • @ref: 91686
  • straininfo: 413994

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23912719Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.Kim YJ, Kim SR, Nguyen NL, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.053819-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25563919Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil.Ngo HTT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0000512015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny29498618Flavobacterium fluviatile sp. nov., isolated from a freshwater creek.Chen WM, Su CL, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0026592018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
31154Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172748228776041
41606Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30632
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91686Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID413994.1
119626Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110819Collection of Institut Pasteur (CIP 110819)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695