Strain identifier
BacDive ID: 16905
Type strain: 
Species: Thermomicrobium roseum
Strain Designation: P-2
Strain history: <- ATCC <- T. Jackson, P-2
NCBI tax ID(s): 309801 (strain), 500 (species)
version 8.1 (current version)
General
@ref: 1898
BacDive-ID: 16905
DSM-Number: 5159
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Thermomicrobium roseum P-2 is a thermophilic, Gram-negative bacterium that was isolated from hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 309801 | strain |
| 500 | species |
strain history
- @ref: 1898
- history: <- ATCC <- T. Jackson, P-2
doi: 10.13145/bacdive16905.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermomicrobiota
- domain: Bacteria
- phylum: Thermomicrobiota
- class: Thermomicrobia
- order: Thermomicrobiales
- family: Thermomicrobiaceae
- genus: Thermomicrobium
- species: Thermomicrobium roseum
- full scientific name: Thermomicrobium roseum Jackson et al. 1973 (Approved Lists 1980)
@ref: 1898
domain: Bacteria
phylum: Thermomicrobia
class: Thermomicrobia
order: Thermomicrobiales
family: Thermomicrobiaceae
genus: Thermomicrobium
species: Thermomicrobium roseum
full scientific name: Thermomicrobium roseum Jackson et al. 1973 emend. Houghton et al. 2015
strain designation: P-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 94.021
Culture and growth conditions
culture medium
- @ref: 1898
- name: THERMOMICROBIUM ROSEUM MEDIUM (DSMZ Medium 592)
- growth: yes
- link: https://mediadive.dsmz.de/medium/592
- composition: Name: THERMOMICROBIUM ROSEUM MEDIUM (DSMZ Medium 592) Composition: Agar 20.0 g/l (NH4)2SO4 1.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.247 g/l CaCl2 x 2 H2O 0.074 g/l Na2B4O7 x 10 H2O 0.044 g/l FeCl3 x 6 H2O 0.019 g/l MnCl2 x 4 H2O 0.018 g/l ZnSO4 x 7 H2O 0.0022 g/l CuCl2 x H2O 0.0005 g/l VOSO4 x 2 H2O 0.0003 g/l Na2MoO4 x 2 H2O 0.0003 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1898 | positive | growth | 70 | thermophilic | |
| 69480 | thermophilic | 99.7 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.967
Isolation, sampling and environmental information
isolation
- @ref: 1898
- sample type: hot spring
- geographic location: Wyoming, Yellowstone Natl. Park
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_7716.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_651;96_3587;97_4405;98_5641;99_7716&stattab=map
- Last taxonomy: Thermomicrobium roseum subclade
- 16S sequence: JQ346739
- Sequence Identity:
- Total samples: 159
- soil counts: 28
- aquatic counts: 104
- animal counts: 18
- plant counts: 9
Safety information
risk assessment
- @ref: 1898
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermomicrobium roseum strain P-2 16S ribosomal RNA gene, partial sequence | JQ346739 | 1371 | ena | 500 |
| 1898 | Thermomicrobium roseum strain ATCC 27502 16S ribosomal RNA gene, complete sequence | M34115 | 1528 | ena | 500 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermomicrobium roseum DSM 5159 | GCA_000021685 | complete | ncbi | 309801 |
| 66792 | Thermomicrobium roseum DSM 5159 | 309801.17 | plasmid | patric | 309801 |
| 66792 | Thermomicrobium roseum DSM 5159 | 309801.4 | complete | patric | 309801 |
| 66792 | Thermomicrobium roseum DSM 5159 | 643348582 | complete | img | 309801 |
GC content
- @ref: 1898
- GC-content: 63
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 77 | no |
| motile | yes | 60.905 | no |
| flagellated | no | 93.164 | no |
| gram-positive | no | 57.222 | no |
| anaerobic | no | 86.494 | no |
| aerobic | yes | 61.25 | no |
| halophile | no | 82.594 | no |
| spore-forming | no | 87.837 | no |
| thermophile | yes | 100 | no |
| glucose-util | yes | 82.492 | no |
| glucose-ferment | no | 83.099 | no |
External links
@ref: 1898
culture collection no.: DSM 5159, ATCC 27502
straininfo link
- @ref: 85910
- straininfo: 47899
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 19148287 | Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. | Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA | PLoS One | 10.1371/journal.pone.0004207 | 2009 | Bacteria, Aerobic, Carbon Monoxide/metabolism, Chemotaxis/genetics, Chloroflexi/classification/*genetics, DNA, Circular, Flagella/genetics, Genome, Bacterial/*genetics, Gram-Negative Bacteria, Hot Springs/microbiology, Metabolic Networks and Pathways, Photosynthesis, Phylogeny, Sequence Analysis, DNA | Phylogeny |
| Enzymology | 22234537 | Characterization and application of fusidane antibiotic biosynethsis enzyme 3-ketosteroid-1-dehydrogenase in steroid transformation. | Chen MM, Wang FQ, Lin LC, Yao K, Wei DZ | Appl Microbiol Biotechnol | 10.1007/s00253-011-3855-5 | 2012 | Aspergillus fumigatus/*enzymology, Biotransformation, Cell Membrane/enzymology, Chloroflexi/genetics, Cytoplasm/enzymology, Escherichia coli/genetics, Gene Expression, Oxidoreductases/genetics/*metabolism, Pichia/genetics, Sequence Alignment, Sequence Homology, Amino Acid, Steroids/*metabolism | Metabolism |
| Phylogeny | 24814334 | Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms. | King CE, King GM | Int J Syst Evol Microbiol | 10.1099/ijs.0.060327-0 | 2014 | Base Composition, *Biofilms, Carbon Monoxide/*metabolism, Chloroflexi/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hawaii, Hot Temperature, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Volcanic Eruptions | Stress |
| Metabolism | 26626227 | Enhancement of soluble expression of codon-optimized Thermomicrobium roseum sarcosine oxidase in Escherichia coli via chaperone co-expression. | Tong Y, Feng S, Xin Y, Yang H, Zhang L, Wang W, Chen W | J Biotechnol | 10.1016/j.jbiotec.2015.11.018 | 2015 | Amino Acid Sequence, Bacterial Proteins/biosynthesis/genetics/metabolism, Base Sequence, Chloroflexi/*enzymology/*genetics, Codon, Escherichia coli/*enzymology/*genetics, Models, Molecular, Molecular Chaperones/genetics/metabolism, Molecular Sequence Data, Phylogeny, Plasmids/genetics, Protein Conformation, Recombinant Proteins/biosynthesis/genetics/metabolism, Sarcosine Oxidase/*biosynthesis/*genetics/metabolism | Enzymology |
| Enzymology | 35134708 | Ancestral sequence reconstruction and spatial structure analysis guided alteration of longer-chain substrate catalysis for Thermomicrobium roseum lipase. | Ma D, Xin Y, Guo Z, Shi Y, Zhang L, Li Y, Gu Z, Ding Z, Shi G | Enzyme Microb Technol | 10.1016/j.enzmictec.2022.109989 | 2022 | Catalysis, *Chloroflexi/enzymology/genetics, Enzyme Stability, *Lipase/metabolism, Substrate Specificity | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1898 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5159) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5159 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 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) | |||
| 85910 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47899.1 | StrainInfo: A central database for resolving microbial strain identifiers |