Strain identifier

BacDive ID: 131176

Type strain: Yes

Species: Lysobacter panacisoli

Strain Designation: CJ29

Strain history: C.-J. Cha CJ29.

NCBI tax ID(s): 1255263 (species)

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General

@ref: 22468

BacDive-ID: 131176

DSM-Number: 101805

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Lysobacter panacisoli CJ29 is a Gram-negative bacterium that was isolated from soil from ginseng field.

NCBI tax id

  • NCBI tax id: 1255263
  • Matching level: species

strain history

@refhistory
22468<- JCM <- C.-J. Cha, Department of Systems Biotechnology, Anseong, Republic of Korea; CJ29
67770C.-J. Cha CJ29.

doi: 10.13145/bacdive131176.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter panacisoli
  • full scientific name: Lysobacter panacisoli Choi et al. 2014

@ref: 22468

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacteraceae, not assigned to order

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter panacisoli

full scientific name: Lysobacter panacisoli Choi et al. 2014

strain designation: CJ29

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 98.235

Culture and growth conditions

culture medium

  • @ref: 22468
  • 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

@refgrowthtypetemperature
22468positivegrowth28
67770positivegrowth30

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no90.449
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22468+----+++--+-++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22468soil from ginseng fieldnear AnseongRepublic of KoreaKORAsia
67770Soil from a ginseng field of Anseong in South Korea

isolation source categories

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

Safety information

risk assessment

  • @ref: 22468
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22468
  • description: Lysobacter panacisoli strain CJ29 16S ribosomal RNA gene, partial sequence
  • accession: JQ806748
  • length: 1311
  • database: nuccore
  • NCBI tax ID: 1255263

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter panacisoli JCM 19212GCA_009765165scaffoldncbi1255263
66792Lysobacter panacisoli strain JCM 192121255263.3wgspatric1255263
66792Lysobacter panacisoli JCM 192122896276005draftimg1255263

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.235no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.244no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.341no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.449no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.839yes
69480flagellatedmotile2+Ability to perform flagellated movementyes67.073no

External links

@ref: 22468

culture collection no.: DSM 101805, JCM 19212, KACC 17502

straininfo link

  • @ref: 89621
  • straininfo: 403185

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24695054Lysobacter panacisoli sp. nov., isolated from ginseng soil.Choi JH, Seok JH, Cha JH, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.062034-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny26111851Lysobacter agri sp. nov., a bacterium isolated from soil.Singh H, Won K, Du J, Yang JE, Akter S, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0510-72015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny29858826Lysobacter pedocola sp. nov., a novel species isolated from Korean soil.Jang JH, Lee D, Seo TJ Microbiol10.1007/s12275-018-8046-y2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Lysobacter/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Phenotype, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride, Soil, *Soil Microbiology, Species Specificity, Temperature, Ubiquinone/analysisPhenotype
Phylogeny31980979Lysobacter prati sp. nov., isolated from a plateau meadow sample.Fang BZ, Xie YG, Zhou XK, Zhang XT, Liu L, Jiao JY, Xiao M, Li WJAntonie Van Leeuwenhoek10.1007/s10482-020-01386-62020Anti-Bacterial Agents/biosynthesis, Bacteriocins/biosynthesis/genetics, China, Fatty Acids/analysis, Genes, Bacterial, Genome, Bacterial, Grassland, *Lysobacter/classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Secondary MetabolismGenetics

Reference

@idauthorstitledoi/urlcatalogue
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
22468Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101805Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101805)
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/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89621Reimer, 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-ID403185.1