Strain identifier

BacDive ID: 7665

Type strain: Yes

Species: Kocuria atrinae

Strain Designation: P30

Strain history: <- JW Bae, KRIBB

NCBI tax ID(s): 592377 (species)

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General

@ref: 17420

BacDive-ID: 7665

DSM-Number: 23883

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

description: Kocuria atrinae P30 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from jeotgal, traditional fermented seafood.

NCBI tax id

  • NCBI tax id: 592377
  • Matching level: species

strain history

@refhistory
17420<- KCTC <- KRIBB
67770J.-W. Bae P30.
67771<- JW Bae, KRIBB

doi: 10.13145/bacdive7665.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria atrinae
  • full scientific name: Kocuria atrinae Park et al. 2010

@ref: 17420

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria atrinae

full scientific name: Kocuria atrinae Park et al. 2010

strain designation: P30

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
29503positive1.25 µmcoccus-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
21417Ivory (1014)10-14 daysISP 2
2141710-14 daysISP 4
21417Golden yellow (1004)10-14 daysISP 5
21417Zinc yellow (1018)10-14 daysISP 7
21417Golden yellow (1004)10-14 daysSuter with tyrosine
21417Zinc yellow (1018)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21417noISP 2
21417noISP 3
21417noISP 4
21417noISP 5
21417noISP 6
21417noISP 7
21417noSuter with tyrosine
21417noSuther without tyrosine

pigmentation

  • @ref: 29503
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17420BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
21417ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21417ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21417ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21417ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21417Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21417Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17420positivegrowth28mesophilic
29503positivegrowth25-37mesophilic
29503positiveoptimum33.5mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29503positivegrowth07-09alkaliphile
29503positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29503aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
21417NaClpositivemaximum10 %
29503NaClpositivegrowth0-4 %
29503NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2141717234glucose+/-
2141717992sucrose+/-
2141718222xylose+/-
2141717268myo-inositol-
2141737684mannose-
2141728757fructose-
2141726546rhamnose+/-
2141716634raffinose-
2141762968cellulose-
2950330089acetate+carbon source
29503286442-oxopentanoate+carbon source
2950322653asparagine+carbon source
2950323652dextrin+carbon source
2950328757fructose+carbon source
2950324265gluconate+carbon source
2950317234glucose+carbon source
2950329987glutamate+carbon source
2950317754glycerol+carbon source
2950317596inosine+carbon source
2950325115malate+carbon source
2950317306maltose+carbon source
2950337684mannose+carbon source
2950317272propionate+carbon source
2950317148putrescine+carbon source
2950315361pyruvate+carbon source
2950351850methyl pyruvate+carbon source
2950333942ribose+carbon source
2950330911sorbitol+carbon source
2950330031succinate+carbon source
2950317748thymidine+carbon source
2950327082trehalose+carbon source
2950353423tween 40+carbon source
2950353426tween 80+carbon source
2950316704uridine+carbon source
2950317151xylitol+carbon source
295034853esculin+hydrolysis
2950317632nitrate+reduction
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation

enzymes

@refvalueactivityec
29503catalase+1.11.1.6
29503urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21417+--+-------++/-+/--+-++/-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21417+/-++/-+-+----+/-+---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17420jeotgal, traditional fermented seafoodRepublic of KoreaKORAsia
67770Korean traditional fermented seafoodRepublic of KoreaKORAsia
67771From Jeotgal, fermented shellfisgRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
174201Risk group (German classification)
21417L1German classification

Sequence information

16S sequences

  • @ref: 17420
  • description: Kocuria atrinae strain P30 16S ribosomal RNA gene, partial sequence
  • accession: FJ607311
  • length: 1472
  • database: ena
  • NCBI tax ID: 592377

GC content

@refGC-contentmethod
1742070.2
6777070.2thermal denaturation, midpoint method (Tm)

External links

@ref: 17420

culture collection no.: DSM 23883, JCM 15914, KCTC 19594

straininfo link

  • @ref: 77109
  • straininfo: 397153

literature

  • topic: Phylogeny
  • Pubmed-ID: 19661502
  • title: Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood.
  • authors: Park EJ, Kim MS, Roh SW, Jung MJ, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014506-0
  • year: 2009
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fermentation, Genes, rRNA, Genotype, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17420Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23883)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23883
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
21417Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23883.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29503Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2590328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
77109Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397153.1StrainInfo: A central database for resolving microbial strain identifiers