Strain identifier

BacDive ID: 133034

Type strain: Yes

Species: Deinococcus budaensis

Strain Designation: FeSTC15-38

Strain history: <- J. Makk, Eötvös Loránd Univ., Microbiology, Budapest, Hungary; FeSTC15-38

NCBI tax ID(s): 1665626 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24822

BacDive-ID: 133034

DSM-Number: 101791

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, sphere-shaped, colony-forming

description: Deinococcus budaensis FeSTC15-38 is an aerobe, Gram-negative, sphere-shaped bacterium that forms circular colonies and was isolated from biofilm from a hydrothermal spring cave wall.

NCBI tax id

  • NCBI tax id: 1665626
  • Matching level: species

strain history

  • @ref: 24822
  • history: <- J. Makk, Eötvös Loránd Univ., Microbiology, Budapest, Hungary; FeSTC15-38

doi: 10.13145/bacdive133034.20240916.9.1

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 budaensis
  • full scientific name: Deinococcus budaensis Makk et al. 2016

@ref: 24822

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus budaensis

full scientific name: Deinococcus budaensis Makk et al. 2016

strain designation: FeSTC15-38

type strain: yes

Morphology

cell morphology

  • @ref: 25080
  • gram stain: negative
  • cell length: 1.8 µm
  • cell width: 1 µm
  • cell shape: sphere-shaped
  • motility: no

colony morphology

  • @ref: 25080
  • colony size: 1.0-2.0 mm
  • colony color: pale pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Sphaerotilus-Leptothrix

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25080Sphaerotilus-Leptothrix agaryes
25080glycerol-yeast extract-peptone mediumyes
25080Reasoner's 2A agar (R2A)yes
25080TGY mediumyes
25080Sphaerotilus-Leptothrixyes
24822GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)yeshttps://mediadive.dsmz.de/medium/1484Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water

culture temp

@refgrowthtypetemperature
25080positivegrowth20.0-37.0
25080positiveoptimum28
24822positivegrowth28

culture pH

@refabilitytypepHPH range
25080positivegrowth6.0-9.0alkaliphile
25080positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25080
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25080
  • spore formation: no

halophily

  • @ref: 25080
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >1.0 %

murein

  • @ref: 25080
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2508017128adipate-assimilation
2508016449alanine-carbon source
25080casein-hydrolysis
2508017634D-glucose-fermentation
2508017634D-glucose-builds acid from
2508017634D-glucose-assimilation
2508017634D-glucose-carbon source
2508016899D-mannitol-assimilation
2508016024D-mannose-assimilation
2508016024D-mannose-carbon source
2508063150D-rhamnose-carbon source
2508016988D-ribose-carbon source
2508065327D-xylose-carbon source
250804853esculin-hydrolysis
250805291gelatin-hydrolysis
2508017754glycerol-carbon source
2508017120hexanoate-assimilation
2508017268myo-inositol-carbon source
2508030849L-arabinose-assimilation
2508030849L-arabinose-carbon source
2508017196L-asparagine-carbon source
2508018050L-glutamine-carbon source
2508017716lactose-carbon source
2508025115malate-assimilation
2508017306maltose-assimilation
25080506227N-acetylglucosamine-assimilation
2508017632nitrate-reduction
2508016301nitrite-reduction
2508018401phenylacetate-assimilation
2508032032potassium gluconate-assimilation
2508053258sodium citrate-assimilation
2508053258sodium citrate-carbon source
2508028017starch-hydrolysis
2508017992sucrose-carbon source
2508027082trehalose-carbon source
2508027897tryptophan-energy source
2508053426tween 80-hydrolysis
2508016199urea-hydrolysis
2508015824D-fructose+carbon source
2508012936D-galactose+carbon source
250805291gelatin+degradation
2508017306maltose+carbon source
2508032954sodium acetate+carbon source
2508050144sodium pyruvate+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2508015688acetoinno
2508016136hydrogen sulfideno
2508035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2508015688acetoin-
2508035581indole-

enzymes

@refvalueactivityec
25080acid phosphatase+3.1.3.2
25080alkaline phosphatase+3.1.3.1
25080alpha-chymotrypsin-3.4.21.1
25080alpha-fucosidase-3.2.1.51
25080alpha-galactosidase-3.2.1.22
25080alpha-glucosidase+3.2.1.20
25080alpha-mannosidase-3.2.1.24
25080arginine dihydrolase+3.5.3.6
25080beta-glucosidase-3.2.1.21
25080beta-glucuronidase+3.2.1.31
25080catalase+1.11.1.6
25080cystine arylamidase-3.4.11.3
25080cytochrome oxidase-1.9.3.1
25080esterase (C 4)+
25080esterase Lipase (C 8)+
25080leucine arylamidase+3.4.11.1
25080lipase (C 14)-
25080N-acetyl-beta-glucosaminidase-3.2.1.52
25080naphthol-AS-BI-phosphohydrolase+
25080phosphatase-
25080trypsin-3.4.21.4
25080tryptophan deaminase-4.1.99.1
25080urease+3.5.1.5
25080valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24822biofilm from a hydrothermal spring cave wallBudapest, Gellért Hill, Rudas-Török spring cave (47.489° N 19.046° E)HungaryHUNEurope47.48919.046
25080Sphaerotilus-Leptothrix agar plates; pH 7.0 (DSMZ Medium 803)l-1: 1.0 g yeast extract, 1.5 g peptone, 0.2 g MgSO4.7H2O, 0.05 g CaCl2 , 0.50 g (NH4)5Fe(C6H4O7)2 , 0.05 g MnSO4 .4H2O, 0.01 g FeCl2 .6H2O and 20.0 g agar5 days28

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Cave water
#Environmental#Aquatic#Thermal spring
#Environmental#Biofilm
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 24822
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24822
  • description: Deinococcus sp. FeSTC15-38 partial 16S rRNA gene, strain FeSTC15-38
  • accession: LN864925
  • length: 1448
  • database: nuccore
  • NCBI tax ID: 1665626

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus budaensis DSM 101791GCA_014201885scaffoldncbi1665626
66792Deinococcus budaensis strain DSM 1017911665626.3wgspatric1665626
66792Deinococcus budaensis DSM 1017912861295632draftimg1665626

GC content

  • @ref: 24822
  • GC-content: 68.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno60no
69480gram-positivegram-positivePositive reaction to Gram-stainingno68.119yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.477yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.885yes
69480spore-formingspore-formingAbility to form endo- or exosporesno72.811yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno80.815yes
69480flagellatedmotile2+Ability to perform flagellated movementno75.69no

External links

@ref: 24822

culture collection no.: DSM 101791, NCAIM B.02630

straininfo link

  • @ref: 91304
  • straininfo: 406501

literature

  • topic: Phylogeny
  • Pubmed-ID: 27667170
  • title: Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave.
  • authors: Makk J, Toth EM, Anda D, Pal S, Schumann P, Kovacs AL, Madl-Szonyi J, Marialigeti K, Borsodi AK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001519
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, *Biofilms, Caves/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Deinococcus/*classification/isolation & purification/radiation effects, Fatty Acids/chemistry, *Gamma Rays, Glycolipids/chemistry, Hungary, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24822Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101791Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101791)
25080J. T. Makk, E. M.,Anda, D.,Pál, S.,Schumann, P.,Kovács, A. L.,Mádl-Szönyi, J.,Márialigeti, K.,Borsodi, A. K.Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave10.1099/ijsem.0.001519IJSEM 66: 5345-5351 201627667170
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91304Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406501.1