Strain identifier

BacDive ID: 134182

Type strain: Yes

Species: Pseudokineococcus marinus

Strain Designation: KST3-3

Strain history: KCCM 42250 <-- S. D. Lee KST3-3.

NCBI tax ID(s): 351215 (species)

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General

@ref: 31725

BacDive-ID: 134182

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, motile, coccus-shaped

description: Pseudokineococcus marinus KST3-3 is an aerobe, Gram-positive, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 351215
  • Matching level: species

strain history

  • @ref: 67770
  • history: KCCM 42250 <-- S. D. Lee KST3-3.

doi: 10.13145/bacdive134182.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Pseudokineococcus
  • species: Pseudokineococcus marinus
  • full scientific name: Pseudokineococcus marinus (Lee 2006) Jurado et al. 2011

  • synonyms

    • @ref: 20215
    • synonym: Kineococcus marinus

@ref: 31725

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Kineosporiales

family: Kineosporiaceae

genus: Pseudokineococcus

species: Pseudokineococcus marinus

strain designation: KST3-3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31725positivecoccus-shapedyes
69480positive100

pigmentation

  • @ref: 31725
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31725positivegrowth04-37
31725positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31725positivegrowth5.1-10.1alkaliphile
31725positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

  • @ref: 31725
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31725no
69481no99
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
31725NaClpositivegrowth01-09 %
31725NaClpositiveoptimum01-04 %

observation

@refobservation
31725aggregates in chains
67770quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3172530089acetate+carbon source
3172516449alanine+carbon source
3172540585alpha-cyclodextrin+carbon source
3172522599arabinose+carbon source
3172518403L-arabitol+carbon source
3172522653asparagine+carbon source
3172517057cellobiose+carbon source
3172523652dextrin+carbon source
3172528757fructose+carbon source
3172533984fucose+carbon source
3172528260galactose+carbon source
3172524175galacturonate+carbon source
3172524265gluconate+carbon source
3172517234glucose+carbon source
3172517716lactose+carbon source
3172517306maltose+carbon source
3172529864mannitol+carbon source
3172516634raffinose+carbon source
3172526546rhamnose+carbon source
3172533942ribose+carbon source
3172517814salicin+carbon source
3172517822serine+carbon source
3172517992sucrose+carbon source
3172527082trehalose+carbon source
3172516704uridine+carbon source
3172517151xylitol+carbon source
317254853esculin+hydrolysis

enzymes

  • @ref: 31725
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
31725marine sediment
67770Sediment of the coast of JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_80905.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_25387;97_31816;98_40758;99_80905&stattab=map
  • Last taxonomy: Pseudokineococcus marinus
  • 16S sequence: DQ200982
  • Sequence Identity:
  • Total samples: 126
  • soil counts: 24
  • aquatic counts: 45
  • animal counts: 39
  • plant counts: 18

Sequence information

16S sequences

  • @ref: 31725
  • description: Kineococcus marinus strain KST3-3 16S ribosomal RNA gene, partial sequence
  • accession: DQ200982
  • length: 1406
  • database: nuccore
  • NCBI tax ID: 351215

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudokineococcus marinus strain JCM 14547351215.3wgspatric351215
67770Pseudokineococcus marinus JCM 14547GCA_013004605contigncbi351215

GC content

@refGC-contentmethod
3172576.6
6777076.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes88.667yes
anaerobicno98.815yes
halophileno74.792no
spore-formingno89.693yes
glucose-utilyes88.956no
motileyes79.717yes
flagellatedno92.742no
thermophileno98.394yes
aerobicyes91.325no
glucose-fermentno81.098no

External links

@ref: 31725

culture collection no.: KCCM 42250, NRRL B-24439, JCM 14547, NBRC 102111

straininfo link

  • @ref: 91780
  • straininfo: 295940

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738104Kineococcus marinus sp. nov., isolated from marine sediment of the coast of Jeju, Korea.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64128-02006Actinomycetales/*classification/genetics/*isolation & purification/ultrastructure, Geologic Sediments/microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyGenetics
Phylogeny19605726Kineococcus rhizosphaerae sp. nov., isolated from rhizosphere soil.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.008599-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisEnzymology
Phylogeny21112988Pseudokineococcus lusitanus gen. nov., sp. nov., and reclassification of Kineococcus marinus Lee 2006 as Pseudokineococcus marinus comb. nov.Jurado V, Laiz L, Ortiz-Martinez A, Groth I, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.026195-02010Actinomycetales/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Environmental Microbiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Portugal, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny32897851Pseudokineococcus galaxeicola sp. nov., isolated from mucus of a stony coral.Li Q, Zheng Y, Guo A, Chen Y, Zhang S, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0044602020Actinobacteria/*classification/isolation & purification, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, China, Coral Reefs, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
31725Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172800128776041
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/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
91780Reimer, 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-ID295940.1