Strain identifier

BacDive ID: 7659

Type strain: Yes

Species: Kocuria himachalensis

Strain Designation: K07-05

Strain history: CIP <- 2006, JCM <- 2005, MTCC

NCBI tax ID(s): 322508 (species)

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

@ref: 12189

BacDive-ID: 7659

DSM-Number: 44905

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

description: Kocuria himachalensis K07-05 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 322508
  • Matching level: species

strain history

@refhistory
12189<- MTCC <- S. Mayilraj; K07-05
67770S. Mayilraj K07-05.
119900CIP <- 2006, JCM <- 2005, MTCC

doi: 10.13145/bacdive7659.20230509.8.1

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 himachalensis
  • full scientific name: Kocuria himachalensis Mayilraj et al. 2006

@ref: 12189

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria himachalensis

full scientific name: Kocuria himachalensis Mayilraj et al. 2006

strain designation: K07-05

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
31622positive1-1.5 µmcoccus-shapedno
119900positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19886Salmon orange10-14 daysISP 2
19886Salmon orange10-14 daysISP 3
19886Salmon orange10-14 daysISP 4
19886Salmon orange10-14 daysISP 5
19886Salmon orange10-14 daysISP 6
19886Salmon orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19886noISP 2
19886noISP 3
19886noISP 4
19886noISP 5
19886noISP 6
19886noISP 7

pigmentation

  • @ref: 31622
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12189TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
19886ISP 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
19886ISP 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:
19886ISP 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
19886ISP 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
19886ISP 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
19886ISP 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
37518MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
119900CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
12189positivegrowth30mesophilic
19886positiveoptimum30mesophilic
31622positivegrowth20-37
31622positiveoptimum30mesophilic
37518positivegrowth30mesophilic
60839positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31622positivegrowth6.5-10alkaliphile
31622positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31622aerobe
60839aerobe
119900obligate aerobe

spore formation

  • @ref: 31622
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31622NaClpositivegrowth0-8 %
31622NaClpositiveoptimum0-8 %

observation

@refobservation
31622aggregates in chains
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3162216449alanine+carbon source
3162229016arginine+carbon source
3162222653asparagine+carbon source
3162235391aspartate+carbon source
3162229987glutamate+carbon source
3162218257ornithine+carbon source
3162215361pyruvate+carbon source
3162233942ribose+carbon source
3162217814salicin+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11990017632nitrate-reduction
11990016301nitrite-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

  • @ref: 119900
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31622catalase+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-
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
68379pyrazinamidase+3.5.1.B15
119900oxidase-
119900catalase+1.11.1.6
119900urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19886-+-+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19886+++-++---+-----+---
119900++--+--+------++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119900-----+----+++/-----+/-------+/-------------+/------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12189soilcold desert of the HimalayasIndiaINDAsia
60839Soilcold desert of the HimalayasIndiaINDAsia
67770Soil of a cold desertIndian HimalayasIndiaINDAsia
119900Environment, SoilHimalayasIndiaINDAsia

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: LC113906
  • 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
121891Risk group (German classification)
198861Risk group (German classification)
1199001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
12189Kocuria himachalensis strain K07-05 16S ribosomal RNA gene, partial sequenceAY9873831459ena322508
67770Kocuria himachalensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13326LC1139061477ena322508

GC content

@refGC-contentmethod
1218975.3
6777075.3thermal denaturation, midpoint method (Tm)

External links

@ref: 12189

culture collection no.: DSM 44905, JCM 13326, MTCC 7020, CCUG 56039, CIP 109344, NCIMB 14351

straininfo link

  • @ref: 77103
  • straininfo: 297238

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
12189Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44905)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44905
19886Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44905.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
31622Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2790828776041
37518Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7075
60839Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56039)https://www.ccug.se/strain?id=56039
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
77103Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297238.1StrainInfo: A central database for resolving microbial strain identifiers
119900Curators of the CIPCollection of Institut Pasteur (CIP 109344)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109344