Strain identifier

BacDive ID: 7650

Type strain: Yes

Species: Kocuria polaris

Strain history: CIP <- 2002, DSMZ <- S. Shivaji: strain CMS 76or <- GI Matsumoto

NCBI tax ID(s): 136273 (species)

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General

@ref: 5330

BacDive-ID: 7650

DSM-Number: 14382

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive

description: Kocuria polaris DSM 14382 is an aerobe, Gram-positive bacterium that was isolated from cyanobacterial mat.

NCBI tax id

  • NCBI tax id: 136273
  • Matching level: species

strain history

@refhistory
5330<- E. Stackebrandt <- S. Shivaji <- G.I. Matsumoto; CMS 76or
67770MTCC 3702 <-- G. S. N. Reddy CMS 76or.
121924CIP <- 2002, DSMZ <- S. Shivaji: strain CMS 76or <- GI Matsumoto

doi: 10.13145/bacdive7650.20240916.9.1

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 polaris
  • full scientific name: Kocuria polaris Reddy et al. 2003

@ref: 5330

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria polaris

full scientific name: Kocuria polaris Reddy et al. 2003

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121924positivecoccus-shapedno
69480no92.5
69480positive94.164

colony morphology

@refcolony colorincubation periodmedium used
18513Vermillion (2002)10-14 daysISP 2
18513Vermillion (2002)10-14 daysISP 3
18513Vermillion (2002)10-14 daysISP 4
18513Vermillion (2002)10-14 daysISP 5
18513Vermillion (2002)10-14 daysISP 6
18513Vermillion (2002)10-14 daysISP 7
121924

multicellular morphology

@refforms multicellular complexmedium name
18513noISP 2
18513noISP 3
18513noISP 4
18513noISP 5
18513noISP 6
18513noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5330TRYPTICASE 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
18513ISP 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
18513ISP 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:
18513ISP 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
18513ISP 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
18513ISP 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
18513ISP 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
33165MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121924CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121924CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperature
18513positiveoptimum28
5330positivegrowth28
33165positivegrowth30
59537positivegrowth22-37
67770positivegrowth20
121924positivegrowth22-37
121924nogrowth41
121924nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59537aerobe
121924obligate aerobe

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1851362968cellulose+
1851316634raffinose+
1851326546rhamnose+
1851328757fructose+
1851329864mannitol+
1851317268myo-inositol+
1851318222xylose-
1851317992sucrose+
1851322599arabinose+
1851317234glucose+
6836817632nitrate-reduction
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
121924606565hippurate+hydrolysis
12192417632nitrate+reduction
12192416301nitrite-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
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12192435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
12192415688acetoin-

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-galactosidase+3.2.1.23
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)+
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
121924oxidase-
121924beta-galactosidase+3.2.1.23
121924alcohol dehydrogenase-1.1.1.1
121924gelatinase-
121924amylase+
121924DNase-
121924caseinase+3.4.21.50
121924catalase+1.11.1.6
121924coagulase-
121924tween esterase-
121924gamma-glutamyltransferase-2.3.2.2
121924lecithinase-
121924lipase-
121924lysine decarboxylase-4.1.1.18
121924ornithine decarboxylase-4.1.1.17
121924phenylalanine ammonia-lyase-4.3.1.24
121924protease-
121924urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18513-+/----++--+-+--+-++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18513+++-+--+---++-+----
121924+++-+----++-+++-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUNO2N2
121924--------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121924+++++-++++++++-++----+++----+--++++++--------++-+++------+--++++++++++-----+---++-------+-++-+-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
5330cyanobacterial matMcMurdo Dry ValleysAustralia and Oceania
59537Cyanobacterial matAustralia and OceaniaAntarcticaATA
67770Cyanobacterial mat from a pond in Antarctica
121924Cyanobacterial materialAntarcticaAntarcticaATA1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Microbial community#Microbial mat
#Host#Microbial#Bacteria

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: AJ278868
  • 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
53301Risk group (German classification)
185131
1219241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Kocuria polaris partial 16S rRNA gene, strain CMS76or
  • accession: AJ278868
  • length: 1480
  • database: nuccore
  • NCBI tax ID: 136273

Genome sequences

  • @ref: 67770
  • description: Kocuria polaris CMS 76or
  • accession: GCA_000786195
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 136273

GC content

  • @ref: 67770
  • GC-content: 72.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes94.164no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.68yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.387no
69480spore-formingspore-formingAbility to form endo- or exosporesno68.136no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.111yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.5no

External links

@ref: 5330

culture collection no.: DSM 14382, CIP 107764, MTCC 3702, CCUG 52397, CMS 76or, JCM 12076, IAM 15066, NBRC 103063

straininfo link

  • @ref: 77094
  • straininfo: 100315

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
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
Phylogeny16902039Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas.Mayilraj S, Kroppenstedt RM, Suresh K, Saini HSInt J Syst Evol Microbiol10.1099/ijs.0.63915-02006Actinobacteria/*classification/isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics
Phylogeny22012251Kocuria sediminis sp. nov., isolated from a marine sediment sample.Bala M, Kaur C, Kaur I, Khan F, Mayilraj SAntonie Van Leeuwenhoek10.1007/s10482-011-9654-22011Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, India, Micrococcaceae/chemistry/classification/genetics/*isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Species SpecificityGenetics
22809716Radio-resistance in psychrotrophic Kocuria sp. ASB 107 isolated from Ab-e-Siah radioactive spring.Asgarani E, Soudi MR, Borzooee F, Dabbagh RJ Environ Radioact10.1016/j.jenvrad.2012.04.0092012Micrococcaceae/*radiation effects, *Radiation, Ionizing, *Ultraviolet Rays
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
Phylogeny26238095Draft genome of Kocuria polaris CMS 76or(T) isolated from cyanobacterial mats, McMurdo Dry Valley, Antarctica: an insight into CspA family of proteins from Kocuria polaris CMS 76or(T).Gundlapally SR, Ara S, Sisinthy SArch Microbiol10.1007/s00203-015-1138-82015Antarctic Regions, Bacterial Proteins/*genetics/metabolism, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial/*genetics, Micrococcaceae/classification/*genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, United StatesGenetics
Phylogeny26362332Kocuria subflava sp. nov., isolated from marine sediment from the Indian Ocean.Jiang Z, Zhang WH, Yuan CG, Chen JY, Cao LX, Park DJ, Xiao M, Kim CJ, Li WJAntonie Van Leeuwenhoek10.1007/s10482-015-0587-z2015Aerobiosis, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Indian Ocean, Locomotion, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5330Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14382)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14382
18513Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14382.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
33165Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5235
59537Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52397)https://www.ccug.se/strain?id=52397
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
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)
77094Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100315.1StrainInfo: A central database for resolving microbial strain identifiers
121924Curators of the CIPCollection of Institut Pasteur (CIP 107764)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107764