Strain identifier

BacDive ID: 17761

Type strain: Yes

Species: Flavisolibacter ginsengiterrae

Strain Designation: GS492

Strain history: CIP <- 2007, KCTC <- W.T. Im, KAIST, Daejon, Korea: strain Gsoil 492

NCBI tax ID(s): 1121885 (strain), 398045 (species)

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General

@ref: 7404

BacDive-ID: 17761

DSM-Number: 18136

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

description: Flavisolibacter ginsengiterrae GS492 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from a ginseng field.

NCBI tax id

NCBI tax idMatching level
398045species
1121885strain

strain history

@refhistory
7404<- S. T. Lee, KAIST; GS492 <- D.-S. An
67771<- ST Lee, KAIST
119628CIP <- 2007, KCTC <- W.T. Im, KAIST, Daejon, Korea: strain Gsoil 492

doi: 10.13145/bacdive17761.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Flavisolibacter
  • species: Flavisolibacter ginsengiterrae
  • full scientific name: Flavisolibacter ginsengiterrae Yoon and Im 2007

@ref: 7404

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Flavisolibacter

species: Flavisolibacter ginsengiterrae

full scientific name: Flavisolibacter ginsengiterrae Yoon and Im 2007 emend. Hahnke et al. 2016

strain designation: GS492

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32127negative0.8 µm0.5 µmrod-shapedno
67771rod-shapedno
67771negative
119628negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7404R2A 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
119628CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7404positivegrowth30mesophilic
32127positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 32127
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32127aerobe
67771aerobe

spore formation

  • @ref: 119628
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32127NaClpositivegrowth0.0-3.0 %
32127NaClpositiveoptimum1.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3212722599arabinose+carbon source
3212733984fucose+carbon source
3212717234glucose+carbon source
3212728087glycogen+carbon source
3212727570histidine+carbon source
3212717306maltose+carbon source
3212737684mannose+carbon source
3212728053melibiose+carbon source
32127506227N-acetylglucosamine+carbon source
3212726271proline+carbon source
3212726546rhamnose+carbon source
3212717814salicin+carbon source
3212717992sucrose+carbon source
321274853esculin+hydrolysis
11962817632nitrate-reduction
11962816301nitrite-reduction

metabolite production

  • @ref: 119628
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32127acid phosphatase+3.1.3.2
32127alkaline phosphatase+3.1.3.1
32127alpha-galactosidase+3.2.1.22
32127gelatinase+
32127cytochrome oxidase+1.9.3.1
119628oxidase+
119628catalase-1.11.1.6
119628urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119628-+++-+++-+++++-+++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7404soil from a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67771From soil, ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
119628Environment, Soil, ginseng cropsPocheonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_18855.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_8945;97_11586;98_14248;99_18855&stattab=map
  • Last taxonomy: Flavisolibacter
  • 16S sequence: AB267476
  • Sequence Identity:
  • Total samples: 1927
  • soil counts: 1482
  • aquatic counts: 201
  • animal counts: 102
  • plant counts: 142

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74041Risk group (German classification)
1196281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7404
  • description: Flavisolibacter ginsengiterrae gene for 16S rRNA, partial sequence, strain: Gsoil 492
  • accession: AB267476
  • length: 1540
  • database: ena
  • NCBI tax ID: 398045

Genome sequences

  • @ref: 66792
  • description: Flavisolibacter ginsengiterrae DSM 18136
  • accession: 2574179725
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1121885

GC content

@refGC-contentmethod
740442.7
3212743
740441.3sequence analysis
6777143.0

External links

@ref: 7404

culture collection no.: DSM 18136, KCTC 12656, Gsoil 492, CIP 109740

straininfo link

  • @ref: 86752
  • straininfo: 309449

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684267Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil.Yoon MH, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.65011-02007Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny20656815Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest.Wang Y, Cai F, Tang Y, Dai J, Qi H, Rahman E, Peng F, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.025221-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Molecular Sequence Data, *Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny24198053Cnuella takakiae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides.Zhao R, Chen XY, Li XD, Tian Y, Kong BH, Chen ZL, Li YHInt J Syst Evol Microbiol10.1099/ijs.0.055749-02013Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Bryophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ice Cover, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25237148Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter.Baik KS, Kim MS, Lee JH, Lee SS, Im WT, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.065664-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26115992Flavisolibacter swuensis sp. nov. isolated from soil.Joo ES, Cha S, Kim MK, Jheong W, Seo T, Srinivasan SJ Microbiol10.1007/s12275-015-5241-y2015Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/genetics, Fatty Acids/analysis, Phenotype, Phosphatidylethanolamines/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisPhenotype
Phylogeny26442990Flavisolibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from soil used for cultivating ginseng.Zhao Y, Liu Q, Kang MS, Jin F, Yu H, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0006602015Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides/*metabolism, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26828023Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil.Lv YY, Wang J, Chen MH, You J, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0009402016Bacterial Typing Techniques, Bacteroidetes/*classification/growth & development/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28632115Flaviaesturariibacter luteus sp. nov., isolated from an agricultural floodplain soil, and emended description of the genus Flaviaesturariibacter.Pascual J, Foesel BU, Geppert A, Huber KJ, Overmann JInt J Syst Evol Microbiol10.1099/ijsem.0.0018542017Agriculture, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Namibia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29671178Flavisolibacter carri sp. nov., isolated from an automotive air-conditioning system.Lee H, Kim DU, Lee S, Kim SG, Park AY, Ahn JH, Ka JOAntonie Van Leeuwenhoek10.1007/s10482-018-1086-92018*Air Conditioning, *Automobiles, Bacteroidetes/genetics/*isolation & purification/metabolism, Genotyping Techniques, Phenotype, Phosphatidylethanolamines/metabolismMetabolism
Phylogeny33742220Flavisolibacter longurius sp. nov., isolated from soil.Maeng S, Park Y, Lee SE, Han JH, Bai J, Kim MKArch Microbiol10.1007/s00203-021-02236-32021Bacteroidetes/classification/genetics/*isolation & purification, Phylogeny, *Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7404Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18136)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18136
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
32127Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2837128776041
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
86752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309449.1StrainInfo: A central database for resolving microbial strain identifiers
119628Curators of the CIPCollection of Institut Pasteur (CIP 109740)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109740