Strain identifier

BacDive ID: 3858

Type strain: Yes

Species: Deinococcus murrayi

Strain Designation: ALT-1b

Strain history: CIP <- 1998, A.C. Ferreira, Dept. Zoologia, Univ. Coimbra, Portugal: strain ALT-1b

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
68910species
1121383strain

strain history

@refhistory
4290<- M.S. da Costa, ALT-1b
121201CIP <- 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

@refgram staincell lengthcell shapemotilityconfidence
23350positive1.2-2.0 µmsphere-shapedno
69480no95.54
69480positive91.078
121201positivecoccus-shapedno

colony morphology

@refcolony sizecolony colorincubation periodmedium used
233500.2 mmorange3 daysDegryse medium 162
121201

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4290NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
4290THERMUS 162 MEDIUM (DSMZ Medium 878)yeshttps://mediadive.dsmz.de/medium/878Name: 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
23350Degryse medium 162yes
39319MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121201CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121201CIP Medium 302yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=302

culture temp

@refgrowthtypetemperaturerange
4290positivegrowth45thermophilic
4290positivegrowth45-50thermophilic
23350positivegrowth30-52.5
23350positiveoptimum47thermophilic
39319positivegrowth45thermophilic
58990positivegrowth37mesophilic
121201positivegrowth30-45
121201nogrowth10psychrophilic
121201nogrowth25mesophilic

culture pH

@refabilitytypepH
23350nogrowth5.0
23350nogrowth10.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58990microaerophile
121201obligate aerobe

spore formation

@refspore formationconfidence
23350no
69481no94
69480no99.886

halophily

@refsaltgrowthtested relationconcentration
121201NaClpositivegrowth0-2 %
121201NaClnogrowth4 %
121201NaClnogrowth6 %
121201NaClnogrowth8 %
121201NaClnogrowth10 %

murein

  • @ref: 4290
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335016947citrate-assimilation
2335017057cellobiose-assimilation
2335012936D-galactose-assimilation
2335016899D-mannitol-assimilation
2335028053melibiose-assimilation
2335016634raffinose-assimilation
2335017924D-sorbitol-assimilation
2335065327D-xylose-assimilation
2335030849L-arabinose-assimilation
2335062345L-rhamnose-assimilation
2335017716lactose-assimilation
2335025115malate-assimilation
2335017268myo-inositol-assimilation
2335015963ribitol-assimilation
2335030031succinate-assimilation
2335017632nitrate-reduction
2335015824D-fructose+assimilation
2335017634D-glucose+assimilation
2335016024D-mannose+assimilation
2335016551D-trehalose+assimilation
2335017754glycerol+assimilation
2335016467L-arginine+assimilation
2335017196L-asparagine+assimilation
2335029985L-glutamate+assimilation
2335018050L-glutamine+assimilation
2335017203L-proline+assimilation
2335017115L-serine+assimilation
2335017306maltose+assimilation
2335015361pyruvate+assimilation
2335017992sucrose+assimilation
2335018305arbutin+degradation
23350casein+degradation
233505291gelatin+degradation
23350606565hippurate+degradation
2335028017starch+degradation
23350yeast extract+required for growth
121201606565hippurate+hydrolysis
12120117632nitrate+reduction
12120116301nitrite-reduction

metabolite production

  • @ref: 121201
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12120115688acetoin-
12120117234glucose-

enzymes

@refvalueactivityec
23350alpha-galactosidase+3.2.1.22
23350beta-galactosidase+3.2.1.23
23350catalase+1.11.1.6
23350cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121201oxidase-
121201beta-galactosidase+3.2.1.23
121201alcohol dehydrogenase-1.1.1.1
121201gelatinase+/-
121201amylase+
121201DNase-
121201caseinase+3.4.21.50
121201catalase+1.11.1.6
121201tween esterase-
121201gamma-glutamyltransferase+2.3.2.2
121201lecithinase-
121201lipase-
121201lysine decarboxylase-4.1.1.18
121201ornithine decarboxylase-4.1.1.17
121201phenylalanine ammonia-lyase-4.3.1.24
121201protease-
121201tryptophan deaminase-
121201urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121201-+++-+--+-++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121201+------+-++-----------+------------+------------------------------------------------------++--+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4290hot springsAlcafachePortugalPRTEurope
121201Environment, Hot springAlcafachePortugalPRTEurope1995

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
42901Risk group (German classification)
1212011Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus murrayi DSM 11303GCA_000482805scaffoldncbi1121383
66792Deinococcus murrayi DSM 113031121383.4wgspatric1121383
66792Deinococcus murrayi DSM 113032527291725draftimg1121383

GC content

  • @ref: 23350
  • GC-content: 69.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno91.264yes
flagellatedno96.784yes
gram-positiveyes82.122yes
anaerobicno98.481no
aerobicyes86.897yes
halophileno87.264no
spore-formingno90.335no
thermophileyes64.213no
glucose-utilyes87.515yes
glucose-fermentno89.994no

External links

@ref: 4290

culture collection no.: DSM 11303, CCUG 50777, CIP 105574

straininfo link

  • @ref: 73368
  • straininfo: 49073

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336890Deinococcus 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 MSInt J Syst Bacteriol10.1099/00207713-47-4-9391997Base 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, TemperatureGenetics
Phylogeny32776869Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil.Wang JJ, Wu SG, Chen Q, Sheng DH, Du ZJ, Li YZInt J Syst Evol Microbiol10.1099/ijsem.0.0043692020Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4290Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11303)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11303
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23350Ana Cristina Ferreira, M. Fernanda Nobre, Fred A. Rainey, Manuel T. Silva, Robin Wait, Jutta Burghardt, Ana Paula Chung, Milton S. Da Costa10.1099/00207713-47-4-939Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot SpringsIJSEM 47: 939-947 19979336890
39319Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17608
58990Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50777)https://www.ccug.se/strain?id=50777
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73368Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49073.1StrainInfo: A central database for resolving microbial strain identifiers
121201Curators of the CIPCollection of Institut Pasteur (CIP 105574)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105574