Strain identifier
BacDive ID: 7328
Type strain: 
Species: Parafrigoribacterium mesophilum
Strain history: <- CJ Kim, KRIBB
NCBI tax ID(s): 433646 (species)
version 8.1 (current version)
General
@ref: 8020
BacDive-ID: 7328
DSM-Number: 19442
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Parafrigoribacterium mesophilum DSM 19442 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, farming field.
NCBI tax id
- NCBI tax id: 433646
- Matching level: species
strain history
| @ref | history |
|---|---|
| 8020 | <- Chang-Jin Kim; MSL 08 |
| 67770 | DSM 19442 <-- C.-J. Kim MSL-08. |
| 67771 | <- CJ Kim, KRIBB |
doi: 10.13145/bacdive7328.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Parafrigoribacterium
- species: Parafrigoribacterium mesophilum
- full scientific name: Parafrigoribacterium mesophilum (Dastager et al. 2008) Kong et al. 2016
synonyms
- @ref: 20215
- synonym: Frigoribacterium mesophilum
@ref: 8020
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Parafrigoribacterium
species: Parafrigoribacterium mesophilum
full scientific name: Parafrigoribacterium mesophilum (Dastager et al. 2008) Kong et al. 2016
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility |
|---|---|---|---|
| 25090 | positive | rod-shaped | yes |
| 32529 | positive | rod-shaped | yes |
| 67771 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 21407 | Beige (1001) | 10-14 days | ISP 2 |
| 21407 | Beige (1001) | 10-14 days | ISP 3 |
| 21407 | Beige (1001) | 10-14 days | ISP 4 |
| 21407 | Beige (1001) | 10-14 days | ISP 5 |
| 21407 | Beige (1001) | 10-14 days | ISP 6 |
| 21407 | Beige (1001) | 10-14 days | ISP 7 |
pigmentation
- @ref: 32529
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 8020 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
| 21407 | 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 | |
| 21407 | 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: | |
| 21407 | 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 | |
| 21407 | 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 | |
| 21407 | 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 | |
| 21407 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8020 | positive | growth | 28 | mesophilic |
| 32529 | positive | growth | 20-28 | |
| 32529 | positive | optimum | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32529 | positive | growth | 6.5-12 | alkaliphile |
| 32529 | positive | optimum | 7.3 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 25090 | aerobe |
| 32529 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation |
|---|---|
| 25090 | no |
| 32529 | no |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32529 | NaCl | positive | growth | 0-3 % |
| 32529 | NaCl | positive | optimum | 0-3 % |
observation
| @ref | observation |
|---|---|
| 32529 | aggregates in chains |
| 67770 | quinones: MK-9 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32529 | 22599 | arabinose | + | carbon source |
| 32529 | 17057 | cellobiose | + | carbon source |
| 32529 | 28260 | galactose | + | carbon source |
| 32529 | 17234 | glucose | + | carbon source |
| 32529 | 17306 | maltose | + | carbon source |
| 32529 | 29864 | mannitol | + | carbon source |
| 32529 | 37684 | mannose | + | carbon source |
| 32529 | 17814 | salicin | + | carbon source |
| 32529 | 17992 | sucrose | + | carbon source |
| 32529 | 27082 | trehalose | + | carbon source |
| 32529 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 32529
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8020 | soil, farming field | Bigeum Island | Republic of Korea | KOR | Asia |
| 67770 | Soil from Bigeum Island | Republic of Korea | KOR | Asia | |
| 67771 | From farming field | Bikeum island | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 8020
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8020
- description: Frigoribacterium mesophilum strain MSL-08 16S ribosomal RNA gene, partial sequence
- accession: EF466126
- length: 1476
- database: ena
- NCBI tax ID: 433646
GC content
| @ref | GC-content | method |
|---|---|---|
| 8020 | 67.5 | |
| 67770 | 67.5 | thermal denaturation, midpoint method (Tm) |
External links
@ref: 8020
culture collection no.: DSM 19442, JCM 19547, KCTC 19311, MSL 08
straininfo link
- @ref: 76778
- straininfo: 398385
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18676471 | Frigoribacterium mesophilum sp. nov., a mesophilic actinobacterium isolated from Bigeum Island, Korea. | Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.65637-0 | 2008 | Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Temperature | Genetics |
| Phylogeny | 24158943 | Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water. | Li AH, Liu HC, Xin YH, Kim SG, Zhou YG | Int J Syst Evol Microbiol | 10.1099/ijs.0.052670-0 | 2013 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Ubiquinone/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 27654623 | Frigoribacterium salinisoli sp. nov., isolated from saline soil, transfer of Frigoribacterium mesophilum to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov. | Kong D, Guo X, Zhou S, Wang H, Wang Y, Zhu J, Dong W, Li Y, He M, Hu G, Zhao B, Ruan Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001504 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 8020 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19442) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19442 | ||||
| 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 | ||||
| 21407 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM19442.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
| 25090 | D. G. Kong, X.,Zhou, S.,Wang, H.,Wang, Y.,Zhu, J.,Dong, W.,Li, Y.,He, M.,Hu, G.,Zhao, B.,Ruan, Z. | 10.1099/ijsem.0.001504 | Frigoribacterium salinisoli sp. nov., isolated from saline soil, transfer of Frigoribacterium mesophilum to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov | IJSEM 66: 5252-5259 2016 | 27654623 | ||
| 32529 | 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 | 28776041 | 28747 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
| 76778 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398385.1 | StrainInfo: A central database for resolving microbial strain identifiers |