Strain identifier

BacDive ID: 17631

Type strain: Yes

Species: Patulibacter ginsengiterrae

Strain Designation: P4-5

Strain history: <- JS Lee, KRIBB

NCBI tax ID(s): 556890 (species)

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General

@ref: 18143

BacDive-ID: 17631

DSM-Number: 25990

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Patulibacter ginsengiterrae P4-5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, ginseng field.

NCBI tax id

  • NCBI tax id: 556890
  • Matching level: species

strain history

@refhistory
18143<- CECT; CECT 7603 <- J.-S. Lee, KCTC; KCTC 19427
67770CECT 7603 <-- J.-S. Lee; KCTC, South Korea; P4-5.
67771<- JS Lee, KRIBB

doi: 10.13145/bacdive17631.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Patulibacteraceae
  • genus: Patulibacter
  • species: Patulibacter ginsengiterrae
  • full scientific name: Patulibacter ginsengiterrae Kim et al. 2012

@ref: 18143

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Patulibacteraceae

genus: Patulibacter

species: Patulibacter ginsengiterrae

full scientific name: Patulibacter ginsengiterrae Kim et al. 2012

strain designation: P4-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30266positive0.8-1 µm0.4-0.6 µmrod-shapedyes
67771positive

pigmentation

  • @ref: 30266
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18143
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
18143positivegrowth25mesophilic
30266positivegrowth05-37
30266positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30266positivegrowth5.5-9.0alkaliphile
30266positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30266aerobe
67771aerobe

spore formation

  • @ref: 30266
  • spore formation: no

halophily

  • @ref: 30266
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: DMK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3026630089acetate+carbon source
3026616449alanine+carbon source
3026622599arabinose+carbon source
3026616947citrate+carbon source
3026633984fucose+carbon source
3026624265gluconate+carbon source
3026617234glucose+carbon source
3026617754glycerol+carbon source
3026628087glycogen+carbon source
3026624996lactate+carbon source
3026625115malate+carbon source
3026617306maltose+carbon source
3026629864mannitol+carbon source
3026637684mannose+carbon source
3026628053melibiose+carbon source
3026626271proline+carbon source
3026617272propionate+carbon source
3026626546rhamnose+carbon source
3026617814salicin+carbon source
3026617822serine+carbon source
3026630911sorbitol+carbon source
3026617992sucrose+carbon source
3026627082trehalose+carbon source
3026618222xylose+carbon source

enzymes

@refvalueactivityec
30266acid phosphatase+3.1.3.2
30266catalase+1.11.1.6
30266cytochrome oxidase+1.9.3.1
30266urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18143soil, ginseng fieldGeumsan CountyRepublic of KoreaKORAsia
67770Soil of a ginseng fieldGeumsan CountyRepublic of KoreaKORAsia
67771From soil of ginseng fieldRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 18143
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18143
  • description: Patulibacter ginsengiterrae strain P4-5 16S ribosomal RNA gene, partial sequence
  • accession: EU710748
  • length: 1455
  • database: ena
  • NCBI tax ID: 556890

GC content

@refGC-contentmethod
1814374.6
6777074.6high performance liquid chromatography (HPLC)

External links

@ref: 18143

culture collection no.: DSM 25990, CECT 7603, KCTC 19427, JCM 31707

straininfo link

  • @ref: 86623
  • straininfo: 379366

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21515709Patulibacter ginsengiterrae sp. nov., isolated from soil of a ginseng field, and an emended description of the genus Patulibacter.Kim KK, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.032052-02011Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23264500Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant.Almeida B, Vaz-Moreira I, Schumann P, Nunes OC, Carvalho G, Crespo MTBInt J Syst Evol Microbiol10.1099/ijs.0.047522-02012Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phosphatidylglycerols/analysis, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/analysis, Waste WaterTranscriptome
Phylogeny27620694Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).Jin D, Kong X, Li H, Luo L, Zhuang X, Zhuang G, Deng Y, Bai ZInt J Syst Evol Microbiol10.1099/ijsem.0.0014692016Bacterial Typing Techniques, Base Composition, Brassica/*microbiology, Cardiolipins/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18143Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25990)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25990
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
30266Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2660728776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
86623Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379366.1StrainInfo: A central database for resolving microbial strain identifiers