Strain identifier

BacDive ID: 7642

Type strain: Yes

Species: Kocuria varians

Strain Designation: G 33, G33

Strain history: CIP <- 1981, CCM <- NCTC, Staphylococcus lactis <- T. Gibson: strain G33

NCBI tax ID(s): 1272 (species)

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General

@ref: 8441

BacDive-ID: 7642

DSM-Number: 20033

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

description: Kocuria varians G 33 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from milk.

NCBI tax id

  • NCBI tax id: 1272
  • Matching level: species

strain history

@refhistory
8441<- CCM <- NCTC <- T. Gibson, G 33 (Staphylococcus lactis)
67770GIFU 9844 <-- ATCC 15306 <-- T. Gibson G33 ("Staphylococcus lactis").
123800CIP <- 1981, CCM <- NCTC, Staphylococcus lactis <- T. Gibson: strain G33

doi: 10.13145/bacdive7642.20230509.8.1

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 varians
  • full scientific name: Kocuria varians (Migula 1900) Stackebrandt et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus varians

@ref: 8441

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria varians

full scientific name: Kocuria varians (Migula 1900) Stackebrandt et al. 1995

strain designation: G 33, G33

type strain: yes

Morphology

cell morphology

  • @ref: 123800
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18619Lemon yellow (1012)10-14 days5006
18619Lemon yellow (1012)10-14 days5425
18619Lemon yellow (1012)10-14 days5428
18619Lemon yellow (1012)10-14 days5530
18619Lemon yellow (1012)10-14 daysISP 2
123800

multicellular morphology

@refforms multicellular complexmedium name
18619noISP 2
18619no5006
18619no5425
18619no5428
18619no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8441CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
18619ISP 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
186195006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
186195425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
186195428yes
186195530yes
37627MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123800CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18619positiveoptimum28mesophilic
8441positivegrowth30mesophilic
37627positivegrowth30mesophilic
67770positivegrowth28mesophilic
123800positivegrowth15-30
123800nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123800
  • oxygen tolerance: facultative anaerobe

murein

  • @ref: 8441
  • murein short key: A11.07
  • type: A3alpha L-Lys-L-Ala4

observation

  • @ref: 67770
  • observation: quinones: MK-7(Hn), MK-7(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123800nitrate+reduction17632
123800nitrite-reduction16301
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose+fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose+fermentation17716
68379sucrose+fermentation17992
68379glycogen+fermentation28087
68375urea-hydrolysis16199
68375arginine-hydrolysis29016
68375ornithine-degradation18257
68375esculin-hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose-fermentation16024
68375maltose-fermentation17306
68375lactose-fermentation17716
68375trehalose-fermentation27082
68375D-mannitol-fermentation16899
68375raffinose-fermentation16634
68375D-ribose-fermentation16988
68375cellobiose-fermentation17057
68375nitrate+reduction17632
68375sucrose-fermentation17992
68375N-acetylglucosamine-fermentation59640
68375turanose-fermentation32528
68375arabinose-fermentation22599

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistant
6837528368novobiocinyesyes1.8 µg
1238000129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12380035581indoleno

metabolite tests

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
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-
68382acid phosphatase+3.1.3.2
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)+
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase+3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5
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
123800beta-galactosidase+3.2.1.23
123800alcohol dehydrogenase-1.1.1.1
123800gelatinase-
123800lecithinase-
123800lysine decarboxylase-4.1.1.18
123800ornithine decarboxylase-4.1.1.17
123800urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18619--+--+++++-+-+-++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18619--+-+----+-++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123800----++/----++++--------------++--+-------+/----------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8441----++--------+-+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123800---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8441milk
67770Milk
123800Food, Milk

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Engineered#Food production#Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_6395.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_481;98_552;99_6395&stattab=map
  • Last taxonomy: Kocuria varians
  • 16S sequence: X87754
  • Sequence Identity:
  • Total samples: 651
  • soil counts: 44
  • aquatic counts: 81
  • animal counts: 516
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84411Risk group (German classification)
186191Hazard group
1238001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kocuria varians 16S ribosomal RNA gene, partial sequenceAF5420741333ena1272
8441M.varians 16S rRNA geneX877541481ena1272

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria varians strain NBRC 153581272.7wgspatric1272
67770Kocuria varians NBRC 15358GCA_006539885contigncbi1272

GC content

@refGC-content
844169.0
6777069

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.117no
gram-positiveyes94.756no
anaerobicno99.466no
aerobicyes89.401no
halophileyes62.521no
spore-formingno93.715no
glucose-utilyes88.746no
flagellatedno98.147no
thermophileno91.361yes
glucose-fermentno64.58yes

External links

@ref: 8441

culture collection no.: DSM 20033, ATCC 15306, CCM 884, NCDO 777, NCTC 7564, JCM 7238, BCRC 12152, CCUG 35392, CCUG 3705, CECT 230, CIP 81.73, GIFU 9844, HAMBI 1951, HAMBI 40, IAM 13594, IFO 15358, LMG 14231, NBRC 15358, NCFB 624, NCFB 777, NCIMB 11697, VKM Ac-2215, VKM B-1232, VKM B-1827, VTT E-97857, NCDO 624

straininfo link

  • @ref: 77086
  • straininfo: 13981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656171Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.Reddy GSN, Prakash JSS, Prabahar V, Matsumoto GI, Stackebrandt E, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.02336-02003Antarctic Regions, Cyanobacteria/isolation & purification, Ecosystem, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Water MicrobiologyEnzymology
Phylogeny30556804Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).Braun MS, Wang E, Zimmermann S, Wagner H, Wink MInt J Syst Evol Microbiol10.1099/ijsem.0.0031702019Animal Structures/*microbiology, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Micrococcaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strigiformes/*microbiology, United States, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8441Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20033)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20033
18619Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20033.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37627Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11238
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68375Automatically annotated from API ID32STA
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
77086Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13981.1StrainInfo: A central database for resolving microbial strain identifiers
123800Curators of the CIPCollection of Institut Pasteur (CIP 81.73)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.73