Strain identifier

BacDive ID: 17489

Type strain: Yes

Species: Lysobacter niastensis

Strain Designation: GH41-7

Strain history: CIP <- 2007, DSMZ <- S. W. Kwon, KACC, Suwon, Korea <- H. Y. Weon, RDA, Suwon, Korea: strain GH41-7

NCBI tax ID(s): 380629 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7554

BacDive-ID: 17489

DSM-Number: 18481

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

description: Lysobacter niastensis GH41-7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil.

NCBI tax id

  • NCBI tax id: 380629
  • Matching level: species

strain history

@refhistory
7554<- S. W. Kwon; GH41-7 <- H.-Y. Weon
121290CIP <- 2007, DSMZ <- S. W. Kwon, KACC, Suwon, Korea <- H. Y. Weon, RDA, Suwon, Korea: strain GH41-7

doi: 10.13145/bacdive17489.20230509.8.1

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 niastensis
  • full scientific name: Lysobacter niastensis Weon et al. 2007

@ref: 7554

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter niastensis

full scientific name: Lysobacter niastensis Weon et al. 2007

strain designation: GH41-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31837negative3 µm0.55 µmrod-shapedyesgliding
69480negative99.987
121290negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7554R2A 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
37775MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121290CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7554positivegrowth28mesophilic
31837positivegrowth10-40
31837positiveoptimum28mesophilic
37775positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31837positivegrowth04-09alkaliphile
31837positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31837aerobe
121290obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.929

halophily

@refsaltgrowthtested relationconcentration
31837NaClpositivegrowth0-1 %
31837NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3183727570histidine+carbon source
3183717306maltose+carbon source
31837506227N-acetylglucosamine+carbon source
318374853esculin+hydrolysis
3183717632nitrate+reduction
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
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
12129017632nitrate+reduction
12129016301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12129035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31837catalase+1.11.1.6
31837gelatinase+
31837cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121290oxidase+
121290catalase+1.11.1.6
121290urease-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
121290-+++-+--+-++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7554+----+++----++------+
7554------++----++------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7554greenhouse soilRepublic of KoreaKORAsia
121290Environment, Soil, greenhouseRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75541Risk group (German classification)
1212901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7554
  • description: Lysobacter niastensis strain GH41-7 16S ribosomal RNA gene, partial sequence
  • accession: DQ462462
  • length: 1468
  • database: ena
  • NCBI tax ID: 380629

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter niastensis DSM 18481GCA_015453285contigncbi380629
66792Lysobacter niastensis strain DSM 18481380629.4wgspatric380629

GC content

  • @ref: 31837
  • GC-content: 66.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.458yes
anaerobicno98.952yes
halophileno96.644yes
spore-formingno95.572no
glucose-utilyes75.875yes
aerobicyes87.065no
motileyes71.577no
flagellatedno88.262yes
thermophileno97.498yes
glucose-fermentno91.138yes

External links

@ref: 7554

culture collection no.: DSM 18481, CIP 109587, KACC 11588

straininfo link

  • @ref: 86487
  • straininfo: 362334

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329782Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea.Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64473-02007DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purificationGenetics
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
Phylogeny19329607Lysobacter ximonensis sp. nov., isolated from soil.Wang Y, Dai J, Zhang L, Luo X, Li Y, Chen G, Tang Y, Meng Y, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.65796-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Lysobacter/*genetics/*isolation & purification/physiology, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Tibet, Ubiquinone/analysisMetabolism
Phylogeny19684312Lysobacter soli sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.016428-02009Base Composition, Base Sequence, Fatty Acids/analysis, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Soil MicrobiologyGenetics
Phylogeny20525815Lysobacter dokdonensis sp. nov., isolated from soil.Oh KH, Kang SJ, Jung YT, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.020495-02010Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Lysobacter/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny20952549Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CXInt J Syst Evol Microbiol10.1099/ijs.0.024448-02010Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phospholipids, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
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
Phylogeny27180096Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0704-72016Base Composition, Caves/*microbiology, China, DNA, Bacterial, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Lysobacter/*classification/genetics/*isolation & purification/metabolism, Nucleic Acid Hybridization, Phenotype, Phospholipids/metabolism, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil MicrobiologyMetabolism
Phylogeny30540245Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0031642018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Tobacco/*microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny31011864Lysobacter caseinilyticus, sp. nov., a casein hydrolyzing bacterium isolated from sea water.Chhetri G, Kim J, Kim I, Seo TAntonie Van Leeuwenhoek10.1007/s10482-019-01267-72019Bacterial Typing Techniques, Base Composition, Caseins/*metabolism, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrolysis, Lysobacter/*classification/genetics/*isolation & purification/metabolism, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Terpenes/analysisMetabolism
Genetics33414313Draft Genome Sequence and Secondary Metabolite Biosynthetic Potential of the Lysobacter niastensis Type Strain DSM 18481.Turrini P, Artuso I, Tescari M, Lugli GA, Frangipani E, Ventura M, Visca PMicrobiol Resour Announc10.1128/MRA.01296-202021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7554Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18481
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
31837Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2810328776041
37775Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7346
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)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86487Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362334.1StrainInfo: A central database for resolving microbial strain identifiers
121290Curators of the CIPCollection of Institut Pasteur (CIP 109587)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109587