Strain identifier

BacDive ID: 3885

Type strain: Yes

Species: Deinococcus ficus

Strain Designation: CC-FR2-10

Strain history: CIP <- 2005, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany: strain CC-FR2-10

NCBI tax ID(s): 1121379 (strain), 317577 (species)

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General

@ref: 7918

BacDive-ID: 3885

DSM-Number: 19119

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Deinococcus ficus CC-FR2-10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere of Ficus religiosa.

NCBI tax id

NCBI tax idMatching level
317577species
1121379strain

strain history

@refhistory
7918<- CCUG <- Lai et al., CC-FR2-10
119344CIP <- 2005, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany: strain CC-FR2-10

doi: 10.13145/bacdive3885.20230509.8.1

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 ficus
  • full scientific name: Deinococcus ficus Lai et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Deinococcus mumbaiensis

@ref: 7918

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus ficus

full scientific name: Deinococcus ficus Lai et al. 2006 emend. Kämpfer 2009

strain designation: CC-FR2-10

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31666positiverod-shapedno
119344positiverod-shapedno

colony morphology

  • @ref: 119344
  • hemolysis ability: 1

pigmentation

  • @ref: 31666
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7918R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
38331MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119344CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7918positivegrowth28mesophilic
31666positivegrowth10-40
31666positiveoptimum37mesophilic
38331positivegrowth30mesophilic
59177positivegrowth22-37

culture pH

@refabilitytypepHPH range
31666positivegrowth5.5-10alkaliphile
31666positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31666aerobe
59177aerobe
119344obligate aerobe

spore formation

@refspore formationconfidence
31666no
69481no100
69480no99.807

observation

  • @ref: 31666
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3166630089acetate+carbon source
3166622599arabinose+carbon source
3166623652dextrin+carbon source
3166628757fructose+carbon source
3166633984fucose+carbon source
3166628260galactose+carbon source
3166624265gluconate+carbon source
3166617234glucose+carbon source
3166624996lactate+carbon source
3166617716lactose+carbon source
3166625115malate+carbon source
3166617306maltose+carbon source
3166629864mannitol+carbon source
3166637684mannose+carbon source
3166628053melibiose+carbon source
31666506227N-acetylglucosamine+carbon source
3166617272propionate+carbon source
3166615361pyruvate+carbon source
3166651850methyl pyruvate+carbon source
3166616634raffinose+carbon source
3166626546rhamnose+carbon source
3166633942ribose+carbon source
3166617822serine+carbon source
3166630911sorbitol+carbon source
3166630031succinate+carbon source
3166617992sucrose+carbon source
3166627082trehalose+carbon source
3166618222xylose+carbon source
11934417632nitrate-reduction
11934416301nitrite-reduction

metabolite production

  • @ref: 119344
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31666cytochrome 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
119344oxidase-
119344alcohol dehydrogenase-1.1.1.1
119344catalase+1.11.1.6
119344lysine decarboxylase-4.1.1.18
119344ornithine decarboxylase-4.1.1.17
119344urease-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
119344-+++-++-++++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
7918rhizosphere of Ficus religiosaFicus religiosaTaiwanTWNAsia
59177Rhizosphere of a fig-tree (Ficus religiosa L.)TaiwanTWNAsia
119344Environment, Rhizosphere of Ficius religiosa L.TaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_2273.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_1228;97_1455;98_1775;99_2273&stattab=map
  • Last taxonomy: Deinococcus ficus subclade
  • 16S sequence: AY941086
  • Sequence Identity:
  • Total samples: 1885
  • soil counts: 240
  • aquatic counts: 386
  • animal counts: 1199
  • plant counts: 60

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
79181Risk group (German classification)
1193441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7918
  • description: Deinococcus ficus strain CC-FR2-10 16S ribosomal RNA gene, partial sequence
  • accession: AY941086
  • length: 1453
  • database: ena
  • NCBI tax ID: 317577

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus ficus CC-FR2-10GCA_003444775completencbi317577
66792Deinococcus ficus DSM 19119GCA_000430865scaffoldncbi1121379
66792Deinococcus ficus DSM 191191121379.3wgspatric1121379
66792Deinococcus ficus DSM 191192524614857draftimg1121379
66792Deinococcus ficus CC-FR2-102739367875completeimg317577

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno84.313yes
flagellatedno91.96yes
gram-positiveyes82.762yes
anaerobicno94.674no
aerobicyes87.06yes
halophileno91.738no
spore-formingno90.608no
glucose-utilyes84.798no
thermophileno94.04yes
glucose-fermentno89.882no

External links

@ref: 7918

culture collection no.: DSM 19119, CCUG 51391, CIP 108832, CCUG 53391

straininfo link

  • @ref: 73395
  • straininfo: 343907

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585695Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L.Lai WA, Kampfer P, Arun AB, Shen FT, Huber B, Rekha PD, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.64007-02006Deinococcus/chemistry/*classification/genetics/*isolation & purification, Ficus/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/analysis/genetics, *Soil MicrobiologyGenetics
Phylogeny19196779Deinococcus mumbaiensis Shashidhar and Bandekar 2006 is a later heterotypic synonym of Deinococcus ficus Lai et al. 2006.Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.002824-02009Classification, Deinococcus/chemistry/*classification, Fatty Acids/analysis, Ficus/microbiology, Species Specificity
Phylogeny25344421Deinococcus enclensis sp. nov., isolated from a marine sediment sample.Thorat MN, Mawlankar R, Sonalkar VV, Venkata Ramana V, Joseph N, Shouche YS, Dastager SGAntonie Van Leeuwenhoek10.1007/s10482-014-0311-42014Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycolipids/analysis, India, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny25351880Deinococcus antarcticus sp. nov., isolated from soil.Dong N, Li HR, Yuan M, Zhang XH, Yu YInt J Syst Evol Microbiol10.1099/ijs.0.066324-02014Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26297659Deinococcus metalli sp. nov., isolated from an abandoned lead-zinc mine.Feng GD, Wang YH, Li YX, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0004392015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Lead, *Mining, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, ZincGenetics
Phylogeny30238338Deinococcus terrigena sp. nov., a novel member of the family Deinococcaceae.Ten LN, Cho H, Cho YJ, Jung HYAntonie Van Leeuwenhoek10.1007/s10482-018-1167-92018Base Composition, Cell Wall/chemistry, Cytosol/chemistry, Deinococcus/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Gamma Rays, Glycolipids/analysis, Hydrogen-Ion Concentration, Korea, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Soil Microbiology, Temperature, Vitamin K 2/analysisEnzymology
32803083Influence of the C-Terminal Tail of RecA Proteins from Alkaline pH-Resistant Bacterium Deinococcus Ficus.Fan HF, Su S, Kuo YA, Chen CJACS Omega10.1021/acsomega.0c028652020

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7918Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19119)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19119
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
31666Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794628776041
38331Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6506
59177Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51391)https://www.ccug.se/strain?id=51391
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
73395Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343907.1StrainInfo: A central database for resolving microbial strain identifiers
119344Curators of the CIPCollection of Institut Pasteur (CIP 108832)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108832