Strain identifier

BacDive ID: 7660

Type strain: Yes

Species: Kocuria aegyptia

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70003

NCBI tax ID(s): 330943 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6686

BacDive-ID: 7660

DSM-Number: 17006

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

description: Kocuria aegyptia CCUG 55750 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 330943
  • Matching level: species

strain history

@refhistory
6686<- W.-J. Li, YIM; YIM 70003
407342003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70003
67770CIP 107966 <-- W. J. Li YIM 70003.
67771<- WJ Li, Yunnan Univ, China
116052CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70003

doi: 10.13145/bacdive7660.20230509.8.1

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 aegyptia
  • full scientific name: Kocuria aegyptia Li et al. 2006

@ref: 6686

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria aegyptia

full scientific name: Kocuria aegyptia Li et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31602positivecoccus-shapedno
67771positive
116052positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18316Beige red (3012)10-14 daysISP 2
18316Beige red (3012)10-14 daysISP 3
18316Beige red (3012)10-14 daysISP 4
18316Beige red (3012)10-14 daysISP 5
18316Beige red (3012)10-14 daysISP 6
18316Beige red (3012)10-14 daysISP 7

pigmentation

  • @ref: 31602
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6686BACTO 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
6686TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
18316ISP 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
18316ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18316ISP 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
18316ISP 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
18316ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18316ISP 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
40734MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116052CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6686positivegrowth28mesophilic
18316positiveoptimum28mesophilic
31602positivegrowth20-40
31602positiveoptimum28mesophilic
40734positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic
116052positivegrowth10-41
116052nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31602positivegrowth05-12alkaliphile
31602positiveoptimum10-10.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31602aerobe
67771aerobe
116052obligate aerobe

spore formation

  • @ref: 31602
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31602NaClpositivegrowth01-05 %
31602NaClpositiveoptimum3 %

observation

@refobservation
31602aggregates in chains
67770quinones: MK-8(H2), MK-9(H2)
67771quinones: MK-8(H2), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160217057cellobiose+carbon source
3160223652dextrin+carbon source
3160228757fructose+carbon source
3160217234glucose+carbon source
3160217306maltose+carbon source
3160237684mannose+carbon source
3160230911sorbitol+carbon source
3160227082trehalose+carbon source
116052606565hippurate+hydrolysis
11605217632nitrate-reduction
11605216301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
11605235581indoleno
116052polysaccharidesno

metabolite tests

  • @ref: 116052
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
31602catalase+1.11.1.6
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
116052oxidase-
116052beta-galactosidase-3.2.1.23
116052alcohol dehydrogenase-1.1.1.1
116052gelatinase-
116052amylase+
116052DNase-
116052caseinase-3.4.21.50
116052catalase+1.11.1.6
116052coagulase-
116052tween esterase-
116052gamma-glutamyltransferase+2.3.2.2
116052lecithinase-
116052lipase-
116052lysine decarboxylase-4.1.1.18
116052ornithine decarboxylase-4.1.1.17
116052phenylalanine ammonia-lyase-4.3.1.24
116052urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18316-+-+--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18316+++-+--+--+---++---
116052-++-+-----+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116052++-----+-----------------------+-+--+------------+-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6686soilEastern dessertEgyptEGYAfrica
60714Soil,saline alkaline desertEastern desertEgyptEGYAfrica2002
67770Saline, alkaline, desert-soilEgyptEGYAfrica
67771saline, alkaline, desert soil from Egypt.EgyptEGYAfrica
116052Environment, SoilEastern desertEgyptEGYAfrica2002

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2760.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_1751;98_2142;99_2760&stattab=map
  • Last taxonomy: Kocuria
  • 16S sequence: DQ059617
  • Sequence Identity:
  • Total samples: 7668
  • soil counts: 1344
  • aquatic counts: 794
  • animal counts: 4476
  • plant counts: 1054

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66861Risk group (German classification)
183161German classification
1160521Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6686
  • description: Kocuria aegyptia strain YIM 70003 16S ribosomal RNA gene, partial sequence
  • accession: DQ059617
  • length: 1492
  • database: ena
  • NCBI tax ID: 330943

GC content

@refGC-contentmethod
668673
6777073thermal denaturation, midpoint method (Tm)
6777173.0thermal denaturation, midpoint method (Tm)

External links

@ref: 6686

culture collection no.: CCUG 55750, CCM 7384, DSM 17006, CCTCC AA 203006, CIP 107966, KCTC 19010, YIM 70003, JCM 14735, NCIMB 14352

straininfo link

  • @ref: 77104
  • straininfo: 232294

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585685Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt.Li WJ, Zhang YQ, Schumann P, Chen HH, Hozzein WN, Tian XP, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63876-02006Actinobacteria/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, *Desert Climate, Egypt, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny26048314Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils.Wang K, Zhang L, Liu Y, Pan Y, Meng L, Xu T, Zhang C, Liu H, Hong S, Huang H, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0003722015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Micrococcaceae/classification, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Soil/chemistry, Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6686Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17006)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17006
18316Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17066.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31602Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789028776041
40734Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5535
60714Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55750)https://www.ccug.se/strain?id=55750
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
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
77104Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232294.1StrainInfo: A central database for resolving microbial strain identifiers
116052Curators of the CIPCollection of Institut Pasteur (CIP 107966)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107966