Strain identifier
BacDive ID: 3847
Type strain: 
Species: Deinococcus grandis
Strain Designation: KS 0485
Strain history: H. Oyaizu KS 0485.
NCBI tax ID(s): 57498 (species)
version 8.1 (current version)
General
@ref: 1532
BacDive-ID: 3847
DSM-Number: 3963
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Deinococcus grandis KS 0485 is a mesophilic, Gram-positive bacterium that was isolated from intestine of Cyprinus carpio.
NCBI tax id
- NCBI tax id: 57498
- Matching level: species
strain history
| @ref | history |
|---|---|
| 1532 | <- E. Stackebrandt <- H. Oyaizu, KS 0485 |
| 67770 | H. Oyaizu KS 0485. |
doi: 10.13145/bacdive3847.20230509.8.1
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 grandis
- full scientific name: Deinococcus grandis (Oyaizu et al. 1987) Rainey et al. 1997
synonyms
- @ref: 20215
- synonym: Deinobacter grandis
@ref: 1532
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Deinococcales
family: Deinococcaceae
genus: Deinococcus
species: Deinococcus grandis
full scientific name: Deinococcus grandis (Oyaizu et al. 1987) Rainey et al. 1997
strain designation: KS 0485
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 1532
- name: PYEA MEDIUM (DSMZ Medium 364)
- growth: yes
- link: https://mediadive.dsmz.de/medium/364
- composition: Name: PYEA MEDIUM (DSMZ Medium 364) Composition: Agar 15.0 g/l Yeast extract 10.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1532 | positive | growth | 26 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.805
murein
- @ref: 1532
- murein short key: A21.01
- type: A3ß L-Orn-Gly2-3
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species |
|---|---|---|
| 1532 | intestine of Cyprinus carpio | Cyprinus carpio |
| 67770 | Intestine of Cyprinus carpio | Cyprinus carpio |
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Host | #Fishes |
| #Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_328.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_228;97_250;98_279;99_328&stattab=map
- Last taxonomy: Deinococcus grandis
- 16S sequence: Y11329
- Sequence Identity:
- Total samples: 1434
- soil counts: 49
- aquatic counts: 717
- animal counts: 577
- plant counts: 91
Safety information
risk assessment
- @ref: 1532
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1532
- description: D.grandis 16S rRNA gene
- accession: Y11329
- length: 1467
- database: ena
- NCBI tax ID: 57498
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Deinococcus grandis ATCC 43672 | GCA_009177165 | complete | ncbi | 57498 |
| 66792 | Deinococcus grandis strain ATCC 43672 | 57498.6 | wgs | patric | 57498 |
| 66792 | Deinococcus grandis strain ATCC43672 | 57498.3 | wgs | patric | 57498 |
| 66792 | Deinococcus grandis ATCC 43672 | 2690315872 | draft | img | 57498 |
| 67770 | Deinococcus grandis ATCC 43672 | GCA_001485435 | contig | ncbi | 57498 |
GC content
- @ref: 1532
- GC-content: 68.7
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 58 | no |
| motile | no | 87.513 | no |
| flagellated | no | 94.053 | no |
| gram-positive | yes | 85.359 | no |
| anaerobic | no | 98.635 | no |
| aerobic | yes | 93.864 | no |
| halophile | no | 94.469 | no |
| spore-forming | no | 88.246 | no |
| thermophile | no | 89.096 | yes |
| glucose-util | yes | 88.732 | no |
| glucose-ferment | no | 90.25 | no |
External links
@ref: 1532
culture collection no.: DSM 3963, ATCC 43672, IAM 13005, JCM 6269, CCM 3997, NBRC 101905, NCIMB 13225
straininfo link
- @ref: 73357
- straininfo: 217748
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15023960 | Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India. | Suresh K, Reddy GSN, Sengupta S, Shivaji S | Int J Syst Evol Microbiol | 10.1099/ijs.0.02758-0 | 2004 | Arsenic/*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/*pharmacology | Genetics |
| Phylogeny | 16585695 | Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. | Lai WA, Kampfer P, Arun AB, Shen FT, Huber B, Rekha PD, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64007-0 | 2006 | Deinococcus/chemistry/*classification/genetics/*isolation & purification, Ficus/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/analysis/genetics, *Soil Microbiology | Genetics |
| Genetics | 19504653 | Development of versatile shuttle vectors for Deinococcus grandis. | Satoh K, Tu Z, Ohba H, Narumi I | Plasmid | 10.1016/j.plasmid.2009.01.005 | 2009 | Amino Acid Sequence, Base Sequence, Deinococcus/*genetics, *Genetic Techniques, Genetic Vectors/*genetics, Luciferases, Firefly/genetics, Molecular Sequence Data, Plasmids/chemistry/genetics, Sequence Alignment, Transformation, Genetic | |
| Phylogeny | 21764979 | Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. | Srinivasan S, Kim MK, Lim S, Joe M, Lee M | Int J Syst Evol Microbiol | 10.1099/ijs.0.033316-0 | 2011 | Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sewage/*microbiology | Metabolism |
| Phylogeny | 27480633 | Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea. | Lee JJ, Lee YH, Park SJ, Lim S, Jeong SW, Lee SY, Cho YJ, Kim MK, Jung HY | J Microbiol | 10.1007/s12275-016-6253-y | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology | Metabolism |
| Phylogeny | 27600000 | Deinococcus saudiensis sp. nov., isolated from desert. | Hussain F, Khan IU, Habib N, Xian WD, Hozzein WN, Zhang ZD, Zhi XY, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001479 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, *Desert Climate, Fatty Acids/chemistry, Gamma Rays, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Saudi Arabia, Sequence Analysis, DNA, *Soil Microbiology, Ultraviolet Rays, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 29095141 | Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower). | Moya G, Yan ZF, Chu DH, Won K, Yang JE, Wang QJ, Kook MC, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002405 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Glycolipids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 31385781 | Deinococcus arcticus sp. nov., isolated from Silene acaulis rhizosphere soil of the Arctic tundra. | Wang XP, Li CM, Yu Y, Li HR, Du ZJ, Mu DS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003636 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/isolation & purification, Fatty Acids/chemistry, Genotype, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Silene/*microbiology, *Soil Microbiology, Svalbard, *Tundra | Genetics |
| Genetics | 31699773 | Complete Genome Sequence of a Radioresistant Bacterial Strain, Deinococcus grandis ATCC 43672. | Shibai A, Satoh K, Kawada M, Kotani H, Narumi I, Furusawa C | Microbiol Resour Announc | 10.1128/MRA.01226-19 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 1532 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3963) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3963 | |
| 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 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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) | |
| 73357 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID217748.1 | StrainInfo: A central database for resolving microbial strain identifiers |