Strain identifier
BacDive ID: 16700
Type strain: 
Species: Meiothermus ruber
Strain Designation: 21
Strain history: <- VKM <- L.G. Loginova, 21
NCBI tax ID(s): 504728 (strain), 277 (species)
version 8.1 (current version)
General
@ref: 602
BacDive-ID: 16700
DSM-Number: 1279
keywords: genome sequence, 16S sequence, Bacteria, thermophilic
description: Meiothermus ruber 21 is a thermophilic bacterium that was isolated from hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 504728 | strain |
| 277 | species |
strain history
- @ref: 602
- history: <- VKM <- L.G. Loginova, 21
doi: 10.13145/bacdive16700.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Thermales
- family: Thermaceae
- genus: Meiothermus
- species: Meiothermus ruber
- full scientific name: Meiothermus ruber (Loginova et al. 1984 ex Loginova et al. 1975) Nobre et al. 1996
synonyms
- @ref: 20215
- synonym: Thermus ruber
@ref: 602
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Meiothermus
species: Meiothermus ruber
full scientific name: Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996
strain designation: 21
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.625 | |
| 69480 | 99.98 | negative |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_1279_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 602
- name: THERMUS RUBER MEDIUM (DSMZ Medium 256)
- growth: yes
- link: https://mediadive.dsmz.de/medium/256
- composition: Name: THERMUS RUBER MEDIUM (DSMZ Medium 256) Composition: Agar 12.0 g/l Universal peptone 5.0 g/l Starch 1.0 g/l Yeast extract 1.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 602 | positive | growth | 50 | thermophilic | |
| 69480 | thermophilic | 98.784 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.995 |
compound production
- @ref: 602
- compound: lytic enzymes
Isolation, sampling and environmental information
isolation
- @ref: 602
- sample type: hot spring
- geographic location: Kamchatka
- country: USSR
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 602
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | T.ruber 16S ribosomal RNA, part | X58346 | 1121 | ena | 504728 |
| 20218 | T.ruber gene for 16S rRNA (partial) | Z15059 | 1430 | ena | 504728 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Meiothermus ruber DSM 1279 | GCA_000376665 | chromosome | ncbi | 504728 |
| 66792 | Meiothermus ruber DSM 1279 | GCA_000024425 | complete | ncbi | 504728 |
| 66792 | Meiothermus ruber DSM 1279 | 504728.6 | complete | patric | 504728 |
| 66792 | Meiothermus ruber DSM 1279 | 504728.9 | complete | patric | 504728 |
| 66792 | Meiothermus ruber DSM 1279 | 2554235408 | complete | img | 504728 |
| 66792 | Meiothermus ruber 21, DSM 1279 | 646564545 | draft | img | 504728 |
GC content
- @ref: 602
- GC-content: 66.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 88.922 | no |
| flagellated | no | 95.238 | no |
| gram-positive | no | 93.267 | no |
| anaerobic | no | 96.924 | no |
| aerobic | yes | 88.804 | no |
| halophile | no | 90.76 | no |
| spore-forming | no | 94.527 | no |
| glucose-util | yes | 85.273 | no |
| thermophile | yes | 99.681 | yes |
| glucose-ferment | no | 91.102 | no |
External links
@ref: 602
culture collection no.: DSM 1279, ATCC 35948, BKM B-1258, VKM B-1258
straininfo link
- @ref: 85719
- straininfo: 41385
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19661497 | Meiothermus cateniformans sp. nov., a slightly thermophilic species from north-eastern China. | Zhang XQ, Zhang WJ, Wei BP, Xu XW, Zhu XF, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.007914-0 | 2009 | Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, China, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Hot Springs/*microbiology, *Hot Temperature, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Enzymology | 23015191 | Characterization of a glycoside hydrolase family 1 beta-galactosidase from hot spring metagenome with transglycosylation activity. | Gupta R, Govil T, Capalash N, Sharma P | Appl Biochem Biotechnol | 10.1007/s12010-012-9889-z | 2012 | Amino Acid Sequence, Bacteria/classification/*enzymology/genetics/isolation & purification, Bacterial Proteins/*chemistry/genetics/metabolism, Enzyme Stability, Hot Springs/*microbiology, Kinetics, *Metagenome, Molecular Sequence Data, Sequence Alignment, beta-Galactosidase/*chemistry/genetics/metabolism | Genetics |
| Genetics | 26641475 | Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches. | Lin HH, Liao YC | PLoS One | 10.1371/journal.pone.0144305 | 2015 | Algorithms, Deinococcus/genetics, Escherichia coli/genetics, *Genome, Microbial, Genomics/*methods, High-Throughput Nucleotide Sequencing/*methods, Pedobacter/genetics, *Software | |
| Phylogeny | 28792366 | Meiothermus luteus sp. nov., a slightly thermophilic bacterium isolated from a hot spring. | Habib N, Khan IU, Hussain F, Zhou EM, Xiao M, Dong L, Zhi XY, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002040 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 602 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1279) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1279 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 85719 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41385.1 | StrainInfo: A central database for resolving microbial strain identifiers |