Strain identifier

BacDive ID: 14413

Type strain: Yes

Species: Jeotgalicoccus marinus

Strain history: <- YG Chen, Yunnan Inst., China

NCBI tax ID(s): 1122128 (strain), 516700 (species)

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General

@ref: 8308

BacDive-ID: 14413

DSM-Number: 19772

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Jeotgalicoccus marinus DSM 19772 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from sea urchin Hemicentrotus pulcherrimus.

NCBI tax id

NCBI tax idMatching level
1122128strain
516700species

strain history

@refhistory
8308<- Y.-G. Chen and S.-K. Tang, YIM; JSM 076033
67771<- YG Chen, Yunnan Inst., China

doi: 10.13145/bacdive14413.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Jeotgalicoccus
  • species: Jeotgalicoccus marinus
  • full scientific name: Jeotgalicoccus marinus Chen et al. 2009

@ref: 8308

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Jeotgalicoccus

species: Jeotgalicoccus marinus

full scientific name: Jeotgalicoccus marinus Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
28951positive0.9 µmcoccus-shapedno
67771coccus-shapedno
67771positive
69480positive100

Culture and growth conditions

culture medium

  • @ref: 8308
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8308positivegrowth28mesophilic
28951positivegrowth10-45
28951positiveoptimum27.5mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
28951positivegrowth6.0-10.0alkaliphile
28951positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28951facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
28951no
67771no
69481no99
69480no99.788

halophily

@refsaltgrowthtested relationconcentration
28951NaClpositivegrowth0.5-25.0 %
28951NaClpositiveoptimum7.5 %

observation

@refobservation
28951aggregates in clumps
67771quinones: MK-7, MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2895116449alanine+carbon source
2895122599arabinose+carbon source
2895129016arginine+carbon source
2895122653asparagine+carbon source
2895117057cellobiose+carbon source
2895116947citrate+carbon source
2895128757fructose+carbon source
2895128260galactose+carbon source
2895117234glucose+carbon source
2895129987glutamate+carbon source
2895117754glycerol+carbon source
2895115428glycine+carbon source
2895125115malate+carbon source
2895117306maltose+carbon source
2895129864mannitol+carbon source
2895137684mannose+carbon source
28951506227N-acetylglucosamine+carbon source
2895126546rhamnose+carbon source
2895117814salicin+carbon source
2895117822serine+carbon source
2895130911sorbitol+carbon source
2895130031succinate+carbon source
2895117151xylitol+carbon source

enzymes

@refvalueactivityec
28951acid phosphatase+3.1.3.2
28951catalase+1.11.1.6
28951cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8308sea urchin Hemicentrotus pulcherrimusHemicentrotus pulcherrimusSouth China SeaChinaCHNAsia
67771From sea waterGuangdong ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_11800.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_5971;97_7182;98_8863;99_11800&stattab=map
  • Last taxonomy: Jeotgalicoccus
  • 16S sequence: EU583727
  • Sequence Identity:
  • Total samples: 12732
  • soil counts: 1053
  • aquatic counts: 876
  • animal counts: 10341
  • plant counts: 462

Safety information

risk assessment

  • @ref: 8308
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8308
  • description: Jeotgalicoccus marinus strain JSM 076033 16S ribosomal RNA gene, partial sequence
  • accession: EU583727
  • length: 1459
  • database: ena
  • NCBI tax ID: 516700

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jeotgalicoccus marinus DSM 19772GCA_000425825scaffoldncbi1122128
66792Jeotgalicoccus marinus DSM 197721122128.4wgspatric1122128
66792Jeotgalicoccus marinus DSM 197722523533549draftimg1122128

GC content

@refGC-contentmethod
830840.3high performance liquid chromatography (HPLC)
2895140.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno89.59no
flagellatedno95.911yes
gram-positiveyes92.926yes
anaerobicno99.195yes
aerobicyes93.936no
halophileyes97.195yes
spore-formingno93.68yes
thermophileno99.808yes
glucose-utilyes79.724no
glucose-fermentno64.369no

External links

@ref: 8308

culture collection no.: DSM 19772, CCTCC AA 207028, KCTC 13189, JSM 076033

straininfo link

  • @ref: 83557
  • straininfo: 408200

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542134Jeotgalicoccus marinus sp. nov., a marine bacterium isolated from a sea urchin.Chen YG, Zhang YQ, Shi JX, Xiao HD, Tang SK, Liu ZX, Huang K, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.002451-02009Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, Species Specificity, Staphylococcaceae/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny19667366Jeotgalicoccus huakuii sp. nov., a halotolerant bacterium isolated from seaside soil.Guo XQ, Li R, Zheng LQ, Lin DQ, Sun JQ, Li SP, Li WJ, Jiang JDInt J Syst Evol Microbiol10.1099/ijs.0.013623-02009Base Composition, China, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Seawater, *Soil Microbiology, Staphylococcaceae/*classification/genetics/isolation & purification/metabolismGenetics
Phylogeny20112668[Diversity of culturable bacteria associated with the sea urchin Hemicentrotus pulcherrimus from Naozhou Island].Huang K, Zhang L, Liu Z, Chen Q, Peng Q, Li W, Cui X, Chen YWei Sheng Wu Xue Bao2009Animals, Bacteria/classification/genetics/*isolation & purification, *Biodiversity, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seawater/*microbiologyGenetics
Phylogeny33724175Jeotgalicoccus meleagridis sp. nov. isolated from bioaerosol from emissions of a turkey fattening plant and reclassification of Jeotgalicoccus halophilus Liu et al. 2011 as a later heterotypic synonym of Jeotgalicoccus aerolatus Martin et al. 2011.Kampfer P, Busse HJ, Glaeser SP, Clermont D, Criscuolo A, Mietke HInt J Syst Evol Microbiol10.1099/ijsem.0.0047452021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8308Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19772)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19772
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
28951Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2539028776041
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
83557Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408200.1StrainInfo: A central database for resolving microbial strain identifiers