Strain identifier
BacDive ID: 3858
Type strain:
Species: Deinococcus murrayi
Strain Designation: ALT-1b
Strain history: CIP <- 1998, A.C. Ferreira, Dept. Zoologia, Univ. Coimbra, Portugal: strain ALT-1b
NCBI tax ID(s): 1121383 (strain), 68910 (species)
General
@ref: 4290
BacDive-ID: 3858
DSM-Number: 11303
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, thermophilic, Gram-positive, sphere-shaped
description: Deinococcus murrayi ALT-1b is a microaerophile, thermophilic, Gram-positive bacterium that was isolated from hot springs.
NCBI tax id
NCBI tax id | Matching level |
---|---|
68910 | species |
1121383 | strain |
strain history
@ref | history |
---|---|
4290 | <- M.S. da Costa, ALT-1b |
121201 | CIP <- 1998, A.C. Ferreira, Dept. Zoologia, Univ. Coimbra, Portugal: strain ALT-1b |
doi: 10.13145/bacdive3858.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Deinococcales
- family: Deinococcaceae
- genus: Deinococcus
- species: Deinococcus murrayi
- full scientific name: Deinococcus murrayi Ferreira et al. 1997
@ref: 4290
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Deinococcales
family: Deinococcaceae
genus: Deinococcus
species: Deinococcus murrayi
full scientific name: Deinococcus murrayi Ferreira et al. 1997
strain designation: ALT-1b
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell shape | motility | confidence |
---|---|---|---|---|---|
23350 | positive | 1.2-2.0 µm | sphere-shaped | no | |
69480 | no | 95.54 | |||
69480 | positive | 91.078 | |||
121201 | positive | coccus-shaped | no |
colony morphology
@ref | colony size | colony color | incubation period | medium used |
---|---|---|---|---|
23350 | 0.2 mm | orange | 3 days | Degryse medium 162 |
121201 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4290 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
4290 | THERMUS 162 MEDIUM (DSMZ Medium 878) | yes | https://mediadive.dsmz.de/medium/878 | Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water |
23350 | Degryse medium 162 | yes | ||
39319 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
121201 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
121201 | CIP Medium 302 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=302 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4290 | positive | growth | 45 | thermophilic |
4290 | positive | growth | 45-50 | thermophilic |
23350 | positive | growth | 30-52.5 | |
23350 | positive | optimum | 47 | thermophilic |
39319 | positive | growth | 45 | thermophilic |
58990 | positive | growth | 37 | mesophilic |
121201 | positive | growth | 30-45 | |
121201 | no | growth | 10 | psychrophilic |
121201 | no | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
23350 | no | growth | 5.0 |
23350 | no | growth | 10.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
58990 | microaerophile |
121201 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
23350 | no | |
69481 | no | 94 |
69480 | no | 99.886 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121201 | NaCl | positive | growth | 0-2 % |
121201 | NaCl | no | growth | 4 % |
121201 | NaCl | no | growth | 6 % |
121201 | NaCl | no | growth | 8 % |
121201 | NaCl | no | growth | 10 % |
murein
- @ref: 4290
- murein short key: A21.01
- type: A3ß L-Orn-Gly2-3
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23350 | 16947 | citrate | - | assimilation |
23350 | 17057 | cellobiose | - | assimilation |
23350 | 12936 | D-galactose | - | assimilation |
23350 | 16899 | D-mannitol | - | assimilation |
23350 | 28053 | melibiose | - | assimilation |
23350 | 16634 | raffinose | - | assimilation |
23350 | 17924 | D-sorbitol | - | assimilation |
23350 | 65327 | D-xylose | - | assimilation |
23350 | 30849 | L-arabinose | - | assimilation |
23350 | 62345 | L-rhamnose | - | assimilation |
23350 | 17716 | lactose | - | assimilation |
23350 | 25115 | malate | - | assimilation |
23350 | 17268 | myo-inositol | - | assimilation |
23350 | 15963 | ribitol | - | assimilation |
23350 | 30031 | succinate | - | assimilation |
23350 | 17632 | nitrate | - | reduction |
23350 | 15824 | D-fructose | + | assimilation |
23350 | 17634 | D-glucose | + | assimilation |
23350 | 16024 | D-mannose | + | assimilation |
23350 | 16551 | D-trehalose | + | assimilation |
23350 | 17754 | glycerol | + | assimilation |
23350 | 16467 | L-arginine | + | assimilation |
23350 | 17196 | L-asparagine | + | assimilation |
23350 | 29985 | L-glutamate | + | assimilation |
23350 | 18050 | L-glutamine | + | assimilation |
23350 | 17203 | L-proline | + | assimilation |
23350 | 17115 | L-serine | + | assimilation |
23350 | 17306 | maltose | + | assimilation |
23350 | 15361 | pyruvate | + | assimilation |
23350 | 17992 | sucrose | + | assimilation |
23350 | 18305 | arbutin | + | degradation |
23350 | casein | + | degradation | |
23350 | 5291 | gelatin | + | degradation |
23350 | 606565 | hippurate | + | degradation |
23350 | 28017 | starch | + | degradation |
23350 | yeast extract | + | required for growth | |
121201 | 606565 | hippurate | + | hydrolysis |
121201 | 17632 | nitrate | + | reduction |
121201 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121201
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121201 | 15688 | acetoin | - | |
121201 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23350 | alpha-galactosidase | + | 3.2.1.22 |
23350 | beta-galactosidase | + | 3.2.1.23 |
23350 | catalase | + | 1.11.1.6 |
23350 | cytochrome oxidase | + | 1.9.3.1 |
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 | 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 | 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) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
121201 | oxidase | - | |
121201 | beta-galactosidase | + | 3.2.1.23 |
121201 | alcohol dehydrogenase | - | 1.1.1.1 |
121201 | gelatinase | +/- | |
121201 | amylase | + | |
121201 | DNase | - | |
121201 | caseinase | + | 3.4.21.50 |
121201 | catalase | + | 1.11.1.6 |
121201 | tween esterase | - | |
121201 | gamma-glutamyltransferase | + | 2.3.2.2 |
121201 | lecithinase | - | |
121201 | lipase | - | |
121201 | lysine decarboxylase | - | 4.1.1.18 |
121201 | ornithine decarboxylase | - | 4.1.1.17 |
121201 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121201 | protease | - | |
121201 | tryptophan deaminase | - | |
121201 | urease | - | 3.5.1.5 |
API zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121201 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121201 | + | - | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
4290 | hot springs | Alcafache | Portugal | PRT | Europe | |
121201 | Environment, Hot spring | Alcafache | Portugal | PRT | Europe | 1995 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Thermal spring |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_1743.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15362;96_993;97_1156;98_1379;99_1743&stattab=map
- Last taxonomy: Deinococcus murrayi subclade
- 16S sequence: Y13041
- Sequence Identity:
- Total samples: 339
- soil counts: 15
- aquatic counts: 45
- animal counts: 262
- plant counts: 17
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4290 | 1 | Risk group (German classification) |
121201 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 4290
- description: D.murrayi 16S rRNA gene, isolate ALT-1bT
- accession: Y13041
- length: 1472
- database: ena
- NCBI tax ID: 68910
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Deinococcus murrayi DSM 11303 | GCA_000482805 | scaffold | ncbi | 1121383 |
66792 | Deinococcus murrayi DSM 11303 | 1121383.4 | wgs | patric | 1121383 |
66792 | Deinococcus murrayi DSM 11303 | 2527291725 | draft | img | 1121383 |
GC content
- @ref: 23350
- GC-content: 69.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 94 | no |
motile | no | 91.264 | yes |
flagellated | no | 96.784 | yes |
gram-positive | yes | 82.122 | yes |
anaerobic | no | 98.481 | no |
aerobic | yes | 86.897 | yes |
halophile | no | 87.264 | no |
spore-forming | no | 90.335 | no |
thermophile | yes | 64.213 | no |
glucose-util | yes | 87.515 | yes |
glucose-ferment | no | 89.994 | no |
External links
@ref: 4290
culture collection no.: DSM 11303, CCUG 50777, CIP 105574
straininfo link
- @ref: 73368
- straininfo: 49073
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9336890 | Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. | Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MS | Int J Syst Bacteriol | 10.1099/00207713-47-4-939 | 1997 | Base Composition, DNA, Bacterial/*analysis, Genes, Bacterial/genetics, Glucose/analysis, Gram-Positive Cocci/chemistry/*classification/*genetics/growth & development/ultrastructure, Hydrogen-Ion Concentration, Lipids/analysis, Microscopy, Electron, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Radiation Tolerance, Temperature | Genetics |
Phylogeny | 32776869 | Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil. | Wang JJ, Wu SG, Chen Q, Sheng DH, Du ZJ, Li YZ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004369 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Deinococcus/*classification/isolation & purification/radiation effects, Fatty Acids/chemistry, Gamma Rays, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ultraviolet Rays, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4290 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11303) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11303 | |||
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 | |||
23350 | Ana Cristina Ferreira, M. Fernanda Nobre, Fred A. Rainey, Manuel T. Silva, Robin Wait, Jutta Burghardt, Ana Paula Chung, Milton S. Da Costa | 10.1099/00207713-47-4-939 | Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot Springs | IJSEM 47: 939-947 1997 | 9336890 | |
39319 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17608 | ||||
58990 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50777) | https://www.ccug.se/strain?id=50777 | |||
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) | |||
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 | |||
73368 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49073.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121201 | Curators of the CIP | Collection of Institut Pasteur (CIP 105574) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105574 |