Strain identifier
BacDive ID: 7659
Type strain:
Species: Kocuria himachalensis
Strain Designation: K07-05
Strain history: CIP <- 2006, JCM <- 2005, MTCC
NCBI tax ID(s): 322508 (species)
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
@ref | history |
---|---|
12189 | <- MTCC <- S. Mayilraj; K07-05 |
67770 | S. Mayilraj K07-05. |
119900 | CIP <- 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
@ref | gram stain | cell length | cell shape | motility |
---|---|---|---|---|
31622 | positive | 1-1.5 µm | coccus-shaped | no |
119900 | positive | coccus-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19886 | Salmon orange | 10-14 days | ISP 2 |
19886 | Salmon orange | 10-14 days | ISP 3 |
19886 | Salmon orange | 10-14 days | ISP 4 |
19886 | Salmon orange | 10-14 days | ISP 5 |
19886 | Salmon orange | 10-14 days | ISP 6 |
19886 | Salmon orange | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19886 | no | ISP 2 |
19886 | no | ISP 3 |
19886 | no | ISP 4 |
19886 | no | ISP 5 |
19886 | no | ISP 6 |
19886 | no | ISP 7 |
pigmentation
- @ref: 31622
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12189 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
19886 | ISP 2 | yes | Name: 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 | |
19886 | ISP 3 | yes | Name: 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: | |
19886 | ISP 4 | yes | Name: 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 | |
19886 | ISP 5 | yes | Name: 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 | |
19886 | ISP 6 | yes | Name: 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 | |
19886 | ISP 7 | yes | Name: 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 | |
37518 | MEDIUM 112 - for Janibacter | yes | Distilled 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 | |
119900 | CIP Medium 112 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12189 | positive | growth | 30 | mesophilic |
19886 | positive | optimum | 30 | mesophilic |
31622 | positive | growth | 20-37 | |
31622 | positive | optimum | 30 | mesophilic |
37518 | positive | growth | 30 | mesophilic |
60839 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31622 | positive | growth | 6.5-10 | alkaliphile |
31622 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31622 | aerobe |
60839 | aerobe |
119900 | obligate aerobe |
spore formation
- @ref: 31622
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31622 | NaCl | positive | growth | 0-8 % |
31622 | NaCl | positive | optimum | 0-8 % |
observation
@ref | observation |
---|---|
31622 | aggregates in chains |
67770 | quinones: MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31622 | 16449 | alanine | + | carbon source |
31622 | 29016 | arginine | + | carbon source |
31622 | 22653 | asparagine | + | carbon source |
31622 | 35391 | aspartate | + | carbon source |
31622 | 29987 | glutamate | + | carbon source |
31622 | 18257 | ornithine | + | carbon source |
31622 | 15361 | pyruvate | + | carbon source |
31622 | 33942 | ribose | + | carbon source |
31622 | 17814 | salicin | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
119900 | 17632 | nitrate | - | reduction |
119900 | 16301 | nitrite | - | reduction |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 119900
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31622 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
119900 | oxidase | - | |
119900 | catalase | + | 1.11.1.6 |
119900 | urease | - | 3.5.1.5 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19886 | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19886 | + | + | + | - | + | + | - | - | - | + | - | - | - | - | - | + | - | - | - | |
119900 | + | + | - | - | + | - | - | + | - | - | - | - | - | - | + | + | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119900 | - | - | - | - | - | + | - | - | - | - | + | + | +/- | - | - | - | - | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12189 | soil | cold desert of the Himalayas | India | IND | Asia |
60839 | Soil | cold desert of the Himalayas | India | IND | Asia |
67770 | Soil of a cold desert | Indian Himalayas | India | IND | Asia |
119900 | Environment, Soil | Himalayas | India | IND | Asia |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
12189 | 1 | Risk group (German classification) |
19886 | 1 | Risk group (German classification) |
119900 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
12189 | Kocuria himachalensis strain K07-05 16S ribosomal RNA gene, partial sequence | AY987383 | 1459 | ena | 322508 |
67770 | Kocuria himachalensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13326 | LC113906 | 1477 | ena | 322508 |
GC content
@ref | GC-content | method |
---|---|---|
12189 | 75.3 | |
67770 | 75.3 | thermal 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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902039 | Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas. | Mayilraj S, Kroppenstedt RM, Suresh K, Saini HS | Int J Syst Evol Microbiol | 10.1099/ijs.0.63915-0 | 2006 | Actinobacteria/*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 Specificity | Genetics |
Phylogeny | 22012251 | Kocuria sediminis sp. nov., isolated from a marine sediment sample. | Bala M, Kaur C, Kaur I, Khan F, Mayilraj S | Antonie Van Leeuwenhoek | 10.1007/s10482-011-9654-2 | 2011 | Carbohydrates/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 Specificity | Genetics |
Phylogeny | 26048314 | Kocuria 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 J | Int J Syst Evol Microbiol | 10.1099/ijs.0.000372 | 2015 | Bacterial 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 Microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12189 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44905) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44905 | |||
19886 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44905.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31622 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27908 | 28776041 | |
37518 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7075 | ||||
60839 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56039) | https://www.ccug.se/strain?id=56039 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
77103 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297238.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119900 | Curators of the CIP | Collection of Institut Pasteur (CIP 109344) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109344 |