Strain identifier

BacDive ID: 11965

Type strain: Yes

Species: Planococcus donghaensis

Strain Designation: JH1

Strain history: <- DH Roh, Chungbuk Natl. Univ.

NCBI tax ID(s): 414778 (species)

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General

@ref: 16172

BacDive-ID: 11965

DSM-Number: 22276

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

description: Planococcus donghaensis JH1 is an aerobe, mesophilic, motile bacterium that was isolated from deep sea sediment.

NCBI tax id

  • NCBI tax id: 414778
  • Matching level: species

strain history

@refhistory
16172<- LMG; LMG 23779 <- D.-H. Roh <- J. H. Choi, Chungbuk Natl. Univ., Republic of Korea; JH1
67771<- DH Roh, Chungbuk Natl. Univ.

doi: 10.13145/bacdive11965.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Planococcus
  • species: Planococcus donghaensis
  • full scientific name: Planococcus donghaensis Choi et al. 2007

@ref: 16172

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus donghaensis

full scientific name: Planococcus donghaensis Choi et al. 2007

strain designation: JH1

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771coccus-shapedyes
67771positive
69480yes94.946
69480positive100

Culture and growth conditions

culture medium

  • @ref: 16172
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16172positivegrowth28mesophilic
67771positivegrowth25-30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
67771no
69481yes95
69480no99.341

murein

  • @ref: 16172
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

observation

  • @ref: 67771
  • observation: quinones: MK-7, MK-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16172deep sea sedimentEast SeaRepublic of KoreaKORAsia
67771From deep-sea sediment of the East SeaRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2782.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_134;99_2782&stattab=map
  • Last taxonomy: Planococcus
  • 16S sequence: EF079063
  • Sequence Identity:
  • Total samples: 1566
  • soil counts: 566
  • aquatic counts: 353
  • animal counts: 550
  • plant counts: 97

Safety information

risk assessment

  • @ref: 16172
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16172
  • description: Planococcus donghaensis strain JH1 16S ribosomal RNA gene, partial sequence
  • accession: EF079063
  • length: 1452
  • database: ena
  • NCBI tax ID: 414778

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus donghaensis DSM 22276GCA_001687665completencbi414778
66792Planococcus donghaensis strain DSM 22276414778.4completepatric414778
66792Planococcus donghaensis strain DSM 22276414778.12plasmidpatric414778
66792Planococcus donghaensis DSM 222762773857989completeimg414778
66792Planococcus donghaensis LMG 237792700988611completeimg414778

GC content

@refGC-content
1617247
6777147.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes95no
flagellatedno55.005no
flagellatedno55.005no
gram-positiveyes92.284yes
gram-positiveyes92.284yes
anaerobicno99.492yes
anaerobicno99.492yes
aerobicyes94.91yes
aerobicyes94.91yes
halophileyes81.418no
halophileyes81.418no
spore-formingyes53.026no
spore-formingyes53.026no
glucose-utilyes89.349no
glucose-utilyes89.349no
thermophileno99.528yes
motileyes82.087yes
motileyes82.087yes
glucose-fermentno89.763no
glucose-fermentno89.763no
thermophileno99.528yes

External links

@ref: 16172

culture collection no.: DSM 22276, KCTC 13050, LMG 23779

straininfo link

  • @ref: 81177
  • straininfo: 292312

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978233Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea.Choi JH, Im WT, Liu QM, Yoo JS, Shin JH, Rhee SK, Roh DHInt J Syst Evol Microbiol10.1099/ijs.0.65036-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Gram-Positive Cocci/*classification/genetics/*isolation & purification/physiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Starch/*metabolismGenetics
Phylogeny26297353Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins.Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PCInt J Syst Evol Microbiol10.1099/ijsem.0.0004232015Animals, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Carotenoids/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylglycerols/chemistry, *Phylogeny, Pigmentation, Planococcus Bacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spheniscidae/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny33973094Planococcus soli sp. nov., isolated from antarctic soil.Zhang S, Ping W, Xin Y, Xin D, Zhang JAntonie Van Leeuwenhoek10.1007/s10482-021-01581-z2021Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, Planococcaceae, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitle
16172Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22276)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22276
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
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
81177Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292312.1StrainInfo: A central database for resolving microbial strain identifiers