Strain identifier

BacDive ID: 7497

Type strain: Yes

Species: Labedella gwakjiensis

Strain Designation: KSW2-17

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 390269 (species)

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General

@ref: 15787

BacDive-ID: 7497

DSM-Number: 21548

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

description: Labedella gwakjiensis KSW2-17 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from dried seaweed.

NCBI tax id

  • NCBI tax id: 390269
  • Matching level: species

strain history

@refhistory
15787<- JCM <- S. D. Lee; KSW2-17
67770S. D. Lee KSW2-17.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive7497.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Labedella
  • species: Labedella gwakjiensis
  • full scientific name: Labedella gwakjiensis Lee 2007

@ref: 15787

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Labedella

species: Labedella gwakjiensis

full scientific name: Labedella gwakjiensis Lee 2007 emend. Nouioui et al. 2018

strain designation: KSW2-17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31882positive2.7 µm0.34 µmrod-shapedno
67771positive
69480positive100

pigmentation

  • @ref: 31882
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15787
  • 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
15787positivegrowth28mesophilic
31882positivegrowth10-37
31882positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31882positivegrowth5.1-10.1alkaliphile
31882positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31882aerobe
67771aerobe

spore formation

@refspore formationconfidence
31882no
69481no100
69480no99.896

halophily

@refsaltgrowthtested relationconcentration
31882NaClpositivegrowth0-5 %
31882NaClpositiveoptimum2.5 %

observation

@refobservation
31882aggregates in clumps
67770quinones: MK-10 (44%), MK-11 (31%)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3188222599arabinose+carbon source
3188217057cellobiose+carbon source
3188228757fructose+carbon source
3188228260galactose+carbon source
318825291gelatin+carbon source
3188217234glucose+carbon source
3188217754glycerol+carbon source
3188217716lactose+carbon source
3188225017leucine+carbon source
3188217306maltose+carbon source
3188229864mannitol+carbon source
3188237684mannose+carbon source
3188237657methyl D-glucoside+carbon source
3188217268myo-inositol+carbon source
3188216634raffinose+carbon source
3188226546rhamnose+carbon source
3188217814salicin+carbon source
3188230911sorbitol+carbon source
3188217992sucrose+carbon source
3188227082trehalose+carbon source
3188218222xylose+carbon source
318824853esculin+hydrolysis

metabolite production

  • @ref: 31882
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31882alpha-galactosidase+3.2.1.22
31882catalase+1.11.1.6
31882gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15787dried seaweedcoast of JejuRepublic of KoreaKORAsia
67770Dried seaweedGwakji Beach in JejuRepublic of KoreaKORAsia
67771From dried seaweedJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2
#Host#Algae
#Engineered#Food production
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 15787
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15787
  • description: Labedella gwakjiensis strain KSW2-17 16S ribosomal RNA gene, partial sequence
  • accession: DQ533552
  • length: 1407
  • database: ena
  • NCBI tax ID: 390269

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Labedella gwakjiensis strain DSM 21548390269.3wgspatric390269
66792Labedella gwakjiensis DSM 215482734482166draftimg390269
67770Labedella gwakjiensis DSM 21548GCA_003014675contigncbi390269
67770Labedella gwakjiensis KSW2-17GCA_003990035contigncbi390269

GC content

@refGC-contentmethod
1578768
6777068high performance liquid chromatography (HPLC)
6777069.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.325yes
anaerobicno99.545yes
halophileno93.171no
spore-formingno91.962no
glucose-utilyes87.083no
aerobicyes93.758yes
motileno88.856yes
flagellatedno97.585yes
thermophileno99.582yes
glucose-fermentno87.975no

External links

@ref: 15787

culture collection no.: DSM 21548, JCM 14008, KCTC 19176, NBRC 106262

straininfo link

  • @ref: 76943
  • straininfo: 319378

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978208Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64591-02007Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny20173001Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.Kim SJ, Lee SSInt J Syst Evol Microbiol10.1099/ijs.0.018788-02010Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aminobutyrates/analysis, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny23203625Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.046599-02012Actinomycetales/*classification/genetics/isolation & purification, *Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny23274994Diaminobutyricimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea.Jang YH, Kim SJ, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-012-2118-12012Actinomycetales/*classification/*genetics/isolation & purification, *Air Microbiology, Phylogeny, RNA, Ribosomal, 16SEnzymology
Phylogeny24132916Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.Kim SJ, Lim JM, Ahn JH, Weon HY, Hamada M, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.058339-02013Acer/*microbiology, Actinomycetales/*classification/genetics/isolation & purification, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny24535740Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae.Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-014-3278-y2014Actinomycetales/classification/*genetics
Phylogeny25331338Labedella endophytica sp. nov., a novel endophytic actinobacterium isolated from stem of Anabasis elatior (C. A. Mey.) Schischk.Wang HF, Zhang YG, Cheng J, Hozzein WN, Liu WH, Li L, Chen JY, Guo JW, Zhang YM, Li WJAntonie Van Leeuwenhoek10.1007/s10482-014-0307-02014Actinobacteria/*classification/*isolation & purification, Amaranthaceae/*microbiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/*isolation & purification, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Ornithine/analysis, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/metabolism, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisEnzymology
Phylogeny31402073Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella.Li FN, Lu Q, Liao SL, Jin T, Li W, Sun CHSyst Appl Microbiol10.1016/j.syapm.2019.1260042019Actinobacteria/chemistry/*classification/genetics, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial/genetics, Genome, Bacterial/genetics, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plants/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15787Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21548)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21548
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
31882Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2814228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
76943Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319378.1StrainInfo: A central database for resolving microbial strain identifiers