Strain identifier

BacDive ID: 3862

Type strain: Yes

Species: Deinococcus indicus

Strain Designation: Wt/1a

Strain history: CIP <- 2004, DSMZ

NCBI tax ID(s): 223556 (species)

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General

@ref: 5838

BacDive-ID: 3862

DSM-Number: 15307

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

description: Deinococcus indicus Wt/1a is an aerobe, mesophilic, Gram-negative bacterium that was isolated from arsenic polluted water, shallow aquifer.

NCBI tax id

  • NCBI tax id: 223556
  • Matching level: species

strain history

@refhistory
5838<- S. Shivaji, CCMB; Wt/1a
339652004, DSMZ
120088CIP <- 2004, DSMZ

doi: 10.13145/bacdive3862.20230509.8.1

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 indicus
  • full scientific name: Deinococcus indicus Suresh et al. 2004

@ref: 5838

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus indicus

full scientific name: Deinococcus indicus Suresh et al. 2004

strain designation: Wt/1a

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29968negativerod-shapedno
120088positiverod-shapedno

colony morphology

  • @ref: 120088

pigmentation

  • @ref: 29968
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5838TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
33965MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
120088CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
5838positivegrowth30mesophilic
29968positivegrowth20-37
29968positiveoptimum30mesophilic
33965positivegrowth30mesophilic
120088positivegrowth25-37mesophilic
120088nogrowth10psychrophilic
120088nogrowth41thermophilic
120088nogrowth45thermophilic

culture pH

  • @ref: 29968
  • ability: positive
  • type: growth
  • pH: 06-07

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29968aerobe
120088obligate aerobe

spore formation

  • @ref: 29968
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29968NaClpositiveoptimum1 %
120088NaClpositivegrowth0 %
120088NaClnogrowth2 %
120088NaClnogrowth4 %
120088NaClnogrowth6 %
120088NaClnogrowth8 %
120088NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2996822599arabinose+carbon source
2996829016arginine+carbon source
2996835391aspartate+carbon source
2996817057cellobiose+carbon source
2996827570histidine+carbon source
2996817716lactose+carbon source
2996817306maltose+carbon source
2996837684mannose+carbon source
2996828053melibiose+carbon source
2996816634raffinose+carbon source
2996826546rhamnose+carbon source
2996833942ribose+carbon source
2996817992sucrose+carbon source
2996816296D-tryptophan+carbon source
299684853esculin+hydrolysis
2996817632nitrate+reduction
120088606565hippurate-hydrolysis
12008817632nitrate-reduction
12008816301nitrite-reduction

metabolite production

  • @ref: 120088
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12008815688acetoin-
12008817234glucose-

enzymes

@refvalueactivityec
29968catalase+1.11.1.6
29968gelatinase+
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
120088oxidase-
120088alcohol dehydrogenase-1.1.1.1
120088gelatinase+
120088amylase+
120088DNase+
120088caseinase+3.4.21.50
120088catalase+1.11.1.6
120088tween esterase-
120088gamma-glutamyltransferase-2.3.2.2
120088lecithinase+
120088lipase+
120088lysine decarboxylase-4.1.1.18
120088ornithine decarboxylase-4.1.1.17
120088phenylalanine ammonia-lyase+4.3.1.24
120088protease+
120088tryptophan deaminase-
120088urease-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
120088-+++-++---++-+-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120088+++++-++-++-+--++-+-+++--------+---+-------------+---------++------------------++---------++-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5838arsenic polluted water, shallow aquiferWest Bengal, Chakdah districtIndiaINDAsia
120088Shallow aquifer in the Bengal basinIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Heavy metal
#Environmental#Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58381Risk group (German classification)
1200881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5838Deinococcus indicus partial 16S rRNA gene, type strain Wt/1aTAJ5491111467ena223556
5838Deinococcus indicus culture DSM:15307 16S ribosomal RNA gene, partial sequenceJQ3467351365ena223556

GC content

  • @ref: 5838
  • GC-content: 65.8

External links

@ref: 5838

culture collection no.: DSM 15307, MTCC 4913, CIP 108415

straininfo link

  • @ref: 73372
  • straininfo: 131417

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023960Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India.Suresh K, Reddy GSN, Sengupta S, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.02758-02004Arsenic/*pharmacology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Deinococcus/classification/drug effects/genetics/*isolation & purification, India, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Water Microbiology, Water Pollutants, Chemical/*pharmacologyGenetics
Phylogeny17684237Deinococcus cellulosilyticus sp. nov., isolated from air.Weon HY, Kim BY, Schumann P, Son JA, Jang J, Go SJ, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.64951-02007*Air Microbiology, Base Composition, DNA, Ribosomal/genetics, Deinococcus/chemistry/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5838Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15307)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15307
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
29968Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2633728776041
33965Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6035
68382Automatically annotated from API zym
73372Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131417.1StrainInfo: A central database for resolving microbial strain identifiers
120088Curators of the CIPCollection of Institut Pasteur (CIP 108415)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108415