Strain identifier
BacDive ID: 7506
Type strain: 
Species: Microcella frigidaquae
Strain Designation: CW1
Strain history: <- CN Seong, Sunchon Natl. Univ.
NCBI tax ID(s): 424758 (species)
version 8.1 (current version)
General
@ref: 17424
BacDive-ID: 7506
DSM-Number: 23889
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Microcella frigidaquae CW1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from cooling water.
NCBI tax id
- NCBI tax id: 424758
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17424 | <- KCTC <- C. N. Seong, Sunchon Natl. Univ., Korea |
| 67770 | C. N. Seong CW1. |
| 67771 | <- CN Seong, Sunchon Natl. Univ. |
doi: 10.13145/bacdive7506.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microcella
- species: Microcella frigidaquae
- full scientific name: Microcella frigidaquae (Baik et al. 2010) Xie et al. 2022
synonyms
- @ref: 20215
- synonym: Chryseoglobus frigidaquae
@ref: 17424
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Micrococcales
family: Microbacteriaceae
genus: Microcella
species: Microcella frigidaquae
full scientific name: Microcella frigidaquae (Baik et al. 2019), Xie et al. 2022
strain designation: CW1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 29577 | positive | rod-shaped | yes | |
| 67771 | positive | |||
| 69480 | positive | 100 |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 21377 | Sand yellow (1002) | 10-14 days | ISP 2 |
| 21377 | Sand yellow (1002) | 10-14 days | ISP 3 |
| 21377 | Broom yellow (1032) | 10-14 days | ISP 4 |
| 21377 | 10-14 days | ISP 5 | |
| 21377 | 10-14 days | ISP 7 | |
| 21377 | 10-14 days | Suter with tyrosine | |
| 21377 | 10-14 days | Suter without tyrosine |
multicellular morphology
| @ref | forms multicellular complex | medium name |
|---|---|---|
| 21377 | no | ISP 2 |
| 21377 | no | ISP 3 |
| 21377 | no | ISP 4 |
| 21377 | no | ISP 5 |
| 21377 | no | ISP 7 |
| 21377 | no | Suter with tyrosine |
| 21377 | no | Suter without tyrosine |
pigmentation
- @ref: 29577
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 17424 | 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 |
| 21377 | 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 | |
| 21377 | 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: | |
| 21377 | 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 | |
| 21377 | 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 | |
| 21377 | 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 | |
| 21377 | Suter with tyrosine | yes | Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes | |
| 21377 | Suter without tyrosine | yes | Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17424 | positive | growth | 28 | mesophilic |
| 29577 | positive | growth | 20-40 | |
| 29577 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29577 | positive | growth | 06-11 | alkaliphile |
| 29577 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 29577 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29577 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.998 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 21377 | NaCl | positive | maximum | 10 % |
| 29577 | NaCl | positive | growth | 0-3 % |
observation
- @ref: 67770
- observation: quinones: MK-13, MK-14, MK-12
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 21377 | 17234 | glucose | - | |
| 21377 | 22599 | arabinose | - | |
| 21377 | 17992 | sucrose | - | |
| 21377 | 18222 | xylose | - | |
| 21377 | 17268 | myo-inositol | - | |
| 21377 | 37684 | mannose | - | |
| 21377 | 28757 | fructose | - | |
| 21377 | 26546 | rhamnose | - | |
| 21377 | 16634 | raffinose | - | |
| 21377 | 62968 | cellulose | + | |
| 29577 | 22599 | arabinose | + | carbon source |
| 29577 | 33942 | ribose | + | carbon source |
| 29577 | 4853 | esculin | + | hydrolysis |
| 68379 | 4853 | esculin | + | hydrolysis |
| 68379 | 16199 | urea | + | hydrolysis |
| 68379 | 5291 | gelatin | + | hydrolysis |
| 68379 | 16988 | D-ribose | - | fermentation |
| 68379 | 65327 | D-xylose | - | fermentation |
| 68379 | 17716 | lactose | - | fermentation |
| 68379 | 17992 | sucrose | - | fermentation |
| 68379 | 28087 | glycogen | - | fermentation |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29577 | catalase | + | 1.11.1.6 |
| 68382 | alpha-fucosidase | - | 3.2.1.51 |
| 68382 | alpha-mannosidase | + | 3.2.1.24 |
| 68382 | alpha-glucosidase | + | 3.2.1.20 |
| 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 | trypsin | + | 3.4.21.4 |
| 68382 | valine arylamidase | + | |
| 68382 | leucine arylamidase | + | 3.4.11.1 |
| 68382 | lipase (C 14) | - | |
| 68382 | esterase lipase (C 8) | + | |
| 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 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21377 | +/- | - | - | - | - | - | + | - | + | + | + | +/- | - | - | +/- | +/- | - | - | - |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21377 | +/- | +/- | + | - | + | + | +/- | + | - | + | - | - | - | - | + | +/- | +/- | + | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17424 | cooling water | Gwangyang | Republic of Korea | KOR | Asia |
| 67770 | Water-cooling system from an oxygen-producing plant | Gwangyang | Republic of Korea | KOR | Asia |
| 67771 | From cooling water | Gwangyang | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_5318.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_3154;98_3963;99_5318&stattab=map
- Last taxonomy: Chryseoglobus frigidaquae subclade
- 16S sequence: EF373534
- Sequence Identity:
- Total samples: 616
- soil counts: 52
- aquatic counts: 417
- animal counts: 139
- plant counts: 8
Safety information
risk assessment
- @ref: 17424
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17424
- description: Chryseoglobus frigidaquae strain CW1 16S ribosomal RNA gene, partial sequence
- accession: EF373534
- length: 1420
- database: ena
- NCBI tax ID: 424758
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microcella frigidaquae DSM 23889 | GCA_014200395 | contig | ncbi | 424758 |
| 66792 | Microcella frigidaquae DSM 23889 | GCA_009664385 | scaffold | ncbi | 424758 |
| 66792 | Chryseoglobus frigidaquae strain DSM 23889 | 424758.4 | wgs | patric | 424758 |
| 66792 | Chryseoglobus frigidaquae strain DSM 23889 | 424758.5 | wgs | patric | 424758 |
| 66792 | Chryseoglobus frigidaquae DSM 23889 | 2845007952 | draft | img | 424758 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17424 | 68.3 | |
| 67770 | 68.3 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 87.84 | yes |
| motile | no | 87.84 | yes |
| flagellated | no | 97.395 | no |
| flagellated | no | 97.395 | no |
| gram-positive | yes | 94.678 | yes |
| gram-positive | yes | 94.678 | yes |
| anaerobic | no | 98.924 | yes |
| anaerobic | no | 98.924 | yes |
| aerobic | yes | 90.477 | no |
| aerobic | yes | 90.477 | no |
| halophile | no | 92.913 | no |
| halophile | no | 92.913 | no |
| spore-forming | no | 93.944 | yes |
| spore-forming | no | 93.944 | yes |
| glucose-util | yes | 84.015 | no |
| glucose-util | yes | 84.015 | no |
| thermophile | no | 98.011 | yes |
| thermophile | no | 98.011 | yes |
| glucose-ferment | no | 87.777 | no |
| glucose-ferment | no | 87.777 | no |
External links
@ref: 17424
culture collection no.: DSM 23889, JCM 14730, KCTC 13142
straininfo link
- @ref: 76952
- straininfo: 402936
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19667371 | Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae. | Baik KS, Park SC, Kim HJ, Lee KH, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.016212-0 | 2009 | Catalase/analysis, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Genotype, Gram-Positive Bacteria/classification/genetics/metabolism/*ultrastructure, Hexoses/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Peptidoglycan/classification, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Republic of Korea | Genetics |
| Phylogeny | 33185523 | Chryseoglobus indicus sp. nov., isolated from deep sea water. | Pei S, Xie F, Wang W, Zhang S, Zhang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004564 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 34628559 | Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov. | Xie F, Pei S, Huang X, Wang L, Kou J, Zhang G | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01668-7 | 2021 | Actinobacteria, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2 | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17424 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23889) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23889 | |||
| 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 | |||
| 21377 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM23889.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
| 29577 | 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 | 25970 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 76952 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402936.1 | StrainInfo: A central database for resolving microbial strain identifiers |