Strain identifier

BacDive ID: 17484

Type strain: Yes

Species: Lysobacter daejeonensis

Strain Designation: GH1-9

Strain history: CIP <- 2006, DSMZ <- S. W. Kwon, KACC <- H.Y. Weon, RDA, Suwon, Korea: strain GH1-9

NCBI tax ID(s): 346181 (species)

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General

@ref: 7098

BacDive-ID: 17484

DSM-Number: 17634

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

description: Lysobacter daejeonensis GH1-9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil.

NCBI tax id

  • NCBI tax id: 346181
  • Matching level: species

strain history

@refhistory
7098<- S.-W. Kwon <- H.-Y. Weon; GH1-9
118843CIP <- 2006, DSMZ <- S. W. Kwon, KACC <- H.Y. Weon, RDA, Suwon, Korea: strain GH1-9

doi: 10.13145/bacdive17484.20230509.8.1

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 daejeonensis
  • full scientific name: Lysobacter daejeonensis Weon et al. 2006

@ref: 7098

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter daejeonensis

full scientific name: Lysobacter daejeonensis Weon et al. 2006

strain designation: GH1-9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31709negative03-04 µm0.4-0.6 µmrod-shapedno
118843negativerod-shapedno

pigmentation

  • @ref: 31709
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7098REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
37503MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
118843CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7098positivegrowth28mesophilic
31709positivegrowth10-37
31709positiveoptimum28mesophilic
37503positivegrowth30mesophilic

culture pH

@refabilitytypepH
31709positivegrowth06-08
31709positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31709aerobe
118843obligate aerobe

spore formation

  • @ref: 31709
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31709NaClpositivegrowth0-3 %
31709NaClpositiveoptimum0-3 %

observation

  • @ref: 31709
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31709370543-hydroxybutyrate+carbon source
3170930089acetate+carbon source
3170917234glucose+carbon source
3170928087glycogen+carbon source
3170917306maltose+carbon source
3170931011valerate+carbon source
317094853esculin+hydrolysis
11884317632nitrate+reduction
11884316301nitrite+reduction

metabolite production

  • @ref: 118843
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31709catalase+1.11.1.6
31709cytochrome oxidase+1.9.3.1
118843oxidase+
118843gelatinase+
118843DNase+
118843catalase-1.11.1.6
118843urease-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
118843-++++++-++++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7098greenhouse soilDaejeonRepublic of KoreaKORAsia
60610Greenhouse soilRepublic of KoreaKORAsia
118843Environment, Greenhouse soilDaejeonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_21672.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_13288;98_16353;99_21672&stattab=map
  • Last taxonomy: Lysobacter
  • 16S sequence: DQ191178
  • Sequence Identity:
  • Total samples: 4904
  • soil counts: 3515
  • aquatic counts: 801
  • animal counts: 191
  • plant counts: 397

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70981Risk group (German classification)
1188431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7098
  • description: Lysobacter daejeonensis strain GH1-9 16S ribosomal RNA gene, partial sequence
  • accession: DQ191178
  • length: 1471
  • database: ena
  • NCBI tax ID: 346181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter daejeonensis GH1-9GCA_000768355contigncbi1385517
66792Lysobacter daejeonensis GH1-91385517.3wgspatric1385517
66792Lysobacter daejeonensis GH1-92627854223draftimg1385517

GC content

@refGC-contentmethod
709861.7high performance liquid chromatography (HPLC)
3170961.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.065yes
gram-positiveno98.623yes
anaerobicno98.989yes
halophileno95.03no
spore-formingno97.041yes
thermophileno98.582yes
glucose-utilyes86.53no
aerobicyes92.111no
flagellatedno97.679yes
glucose-fermentno91.048no

External links

@ref: 7098

culture collection no.: CCUG 55492, KACC 11406, DSM 17634, CIP 109292

straininfo link

@refstraininfo
86481290982
86482410854

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627636Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils.Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW, Stackebrandt E, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.64095-02006Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/chemistry/*classification/*isolation & purification/physiologyEnzymology
Phylogeny19329586Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.).Aslam Z, Yasir M, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.000588-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny20400661Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil.Wang GL, Wang L, Chen HH, Shen B, Li SP, Jiang JDInt J Syst Evol Microbiol10.1099/ijs.0.020990-02010Base Composition, Biotransformation, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nitriles/*metabolism, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25510974Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory.Ye XM, Chu CW, Shi C, Zhu JC, He Q, He JInt J Syst Evol Microbiol10.1099/ijs.0.0000242014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Pesticides, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry, Waste Disposal, FluidGenetics
Phylogeny26483081Lysobacter chengduensis sp. nov. Isolated from the Air of Captive Ailuropoda melanoleuca Enclosures in Chengdu, China.Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R, Yan Q, Hou RCurr Microbiol10.1007/s00284-015-0921-82016Aerobiosis, *Air Microbiology, Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ursidae/*microbiologyGenetics
Phylogeny26746421Lysobacter aestuarii sp. nov., isolated from estuary sediment.Jeong SE, Lee HJ, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0008842016
Phylogeny28984550Lysobacter olei sp. nov., isolated from oil-contaminated soil.Chaudhary DK, Lee SD, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0023482017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Ubiquinone/chemistryTranscriptome
Phylogeny30758281Lysobacter psychrotolerans sp. nov., isolated from soil in the Tianshan Mountains, Xinjiang, China.Luo Y, Dong H, Zhou M, Huang Y, Zhang H, He W, Sheng H, An LInt J Syst Evol Microbiol10.1099/ijsem.0.0032132019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, Fatty Acids/chemistry, Lysobacter/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7098Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17634
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
31709Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2798628776041
37503Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7018
60610Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55492)https://www.ccug.se/strain?id=55492
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)
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
86481Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290982.1StrainInfo: A central database for resolving microbial strain identifiers
86482Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID410854.1StrainInfo: A central database for resolving microbial strain identifiers
118843Curators of the CIPCollection of Institut Pasteur (CIP 109292)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109292