Strain identifier
BacDive ID: 7660
Type strain:
Species: Kocuria aegyptia
Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70003
NCBI tax ID(s): 330943 (species)
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
@ref | history |
---|---|
6686 | <- W.-J. Li, YIM; YIM 70003 |
40734 | 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70003 |
67770 | CIP 107966 <-- W. J. Li YIM 70003. |
67771 | <- WJ Li, Yunnan Univ, China |
116052 | CIP <- 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
@ref | gram stain | cell shape | motility |
---|---|---|---|
31602 | positive | coccus-shaped | no |
67771 | positive | ||
116052 | positive | coccus-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18316 | Beige red (3012) | 10-14 days | ISP 2 |
18316 | Beige red (3012) | 10-14 days | ISP 3 |
18316 | Beige red (3012) | 10-14 days | ISP 4 |
18316 | Beige red (3012) | 10-14 days | ISP 5 |
18316 | Beige red (3012) | 10-14 days | ISP 6 |
18316 | Beige red (3012) | 10-14 days | ISP 7 |
pigmentation
- @ref: 31602
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6686 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: 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 |
6686 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
18316 | 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 | |
18316 | 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: | |
18316 | 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 | |
18316 | 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 | |
18316 | 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 | |
18316 | 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 | |
40734 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
116052 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6686 | positive | growth | 28 | mesophilic |
18316 | positive | optimum | 28 | mesophilic |
31602 | positive | growth | 20-40 | |
31602 | positive | optimum | 28 | mesophilic |
40734 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
116052 | positive | growth | 10-41 | |
116052 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31602 | positive | growth | 05-12 | alkaliphile |
31602 | positive | optimum | 10-10.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31602 | aerobe |
67771 | aerobe |
116052 | obligate aerobe |
spore formation
- @ref: 31602
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31602 | NaCl | positive | growth | 01-05 % |
31602 | NaCl | positive | optimum | 3 % |
observation
@ref | observation |
---|---|
31602 | aggregates in chains |
67770 | quinones: MK-8(H2), MK-9(H2) |
67771 | quinones: MK-8(H2), MK-9(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31602 | 17057 | cellobiose | + | carbon source |
31602 | 23652 | dextrin | + | carbon source |
31602 | 28757 | fructose | + | carbon source |
31602 | 17234 | glucose | + | carbon source |
31602 | 17306 | maltose | + | carbon source |
31602 | 37684 | mannose | + | carbon source |
31602 | 30911 | sorbitol | + | carbon source |
31602 | 27082 | trehalose | + | carbon source |
116052 | 606565 | hippurate | + | hydrolysis |
116052 | 17632 | nitrate | - | reduction |
116052 | 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 | Chebi-ID | metabolite | production |
---|---|---|---|
116052 | 35581 | indole | no |
116052 | polysaccharides | no |
metabolite tests
- @ref: 116052
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
31602 | 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 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
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 |
116052 | oxidase | - | |
116052 | beta-galactosidase | - | 3.2.1.23 |
116052 | alcohol dehydrogenase | - | 1.1.1.1 |
116052 | gelatinase | - | |
116052 | amylase | + | |
116052 | DNase | - | |
116052 | caseinase | - | 3.4.21.50 |
116052 | catalase | + | 1.11.1.6 |
116052 | coagulase | - | |
116052 | tween esterase | - | |
116052 | gamma-glutamyltransferase | + | 2.3.2.2 |
116052 | lecithinase | - | |
116052 | lipase | - | |
116052 | lysine decarboxylase | - | 4.1.1.18 |
116052 | ornithine decarboxylase | - | 4.1.1.17 |
116052 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116052 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18316 | - | + | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18316 | + | + | + | - | + | - | - | + | - | - | + | - | - | - | + | + | - | - | - | |
116052 | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116052 | + | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
6686 | soil | Eastern dessert | Egypt | EGY | Africa | ||
60714 | Soil,saline alkaline desert | Eastern desert | Egypt | EGY | Africa | 2002 | |
67770 | Saline, alkaline, desert-soil | Egypt | EGY | Africa | |||
67771 | saline, alkaline, desert soil from Egypt. | Egypt | EGY | Africa | |||
116052 | Environment, Soil | Eastern desert | Egypt | EGY | Africa | 2002 |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
6686 | 1 | Risk group (German classification) |
18316 | 1 | German classification |
116052 | 1 | Risk 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
@ref | GC-content | method |
---|---|---|
6686 | 73 | |
67770 | 73 | thermal denaturation, midpoint method (Tm) |
67771 | 73.0 | thermal 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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16585685 | Kocuria 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 CL | Int J Syst Evol Microbiol | 10.1099/ijs.0.63876-0 | 2006 | Actinobacteria/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 Microbiology | 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 |
---|---|---|---|---|---|---|
6686 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17006) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17006 | |||
18316 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM17066.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 | |||
31602 | 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 | 27890 | 28776041 | |
40734 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5535 | ||||
60714 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55750) | https://www.ccug.se/strain?id=55750 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
77104 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232294.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116052 | Curators of the CIP | Collection of Institut Pasteur (CIP 107966) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107966 |