Deinococcus grandis (DSM 3963, ATCC 43672, IAM 13005)

Name: Deinococcus grandis (DSM 3963, ATCC 43672, IAM 13005)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3847

Type strain

Strain Designation KS 0485

Culture col. no. DSM 3963 ATCC 43672 IAM 13005 KS 0485 JCM 6269 3 more

NCBI tax ID(s) 57498

Special Collections DSMZ JCM

History DSMZ <- E. Stackebrandt <- H. Oyaizu, KS 0485 JCM <-- H. Oyaizu KS 0485.

Links

Deinococcus grandis KS 0485 is a bacterium that was isolated from intestine of Cyprinus carpio.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 217748

ATCC 43672,IAM 13005,JCM 6269,DSM 3963,CCM 3997,NCIMB 13225,HAMBI 2161,NBRC 101905,BCRC 17376,CCRC 17376

@ref 20215

Last LPSN update 2026-05-29 08:25:48

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 (1)

Deinobacter grandis

BacDive ID	Other strains from **Deinococcus grandis** (3)	Type strain
3848	D. grandis KS 0460, DSM 3964, IAM 13006, JCM 6270, CCM ...
3849	D. grandis KS 0488, DSM 3965, IAM 13007, JCM 6271
3850	D. grandis KS 0492, DSM 3966, IAM 13008, JCM 6272, CCM ...

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		97.362
125439		99.685	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1532	PYEA MEDIUM (DSMZ Medium 364)		Medium recipe at MediaDive	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 (°C)
1532	positive	growth	26
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	98.109

Spore formation

@ref	Spore formation	Confidence
125439		96.162

Murein

@ref	Murein short key	Type
1532	A21.01	A3ß L-Orn-Gly₂_-₃

Observation

67770

Observationquinones: MK-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Host Body-Site	#Gastrointestinal tract

Isolation

@ref	Sample type	Host species
1532	intestine of Cyprinus carpio	Cyprinus carpio
67770	Intestine of Cyprinus carpio	Cyprinus carpio

Taxonmaps

69479

Global distribution of 16S sequence Y11329 (>99% sequence identity) for Deinococcus grandis from Microbeatlas

Aquatic Samples	717
Soil Samples	49
Animal Samples	577
Plant Samples	91
Total Samples	1434

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1532	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM148543v1 assembly for Deinococcus grandis ATCC 43672	contig	GCA_001485435	57498.3	2690315872	57498	76.94
66792	ASM917716v1 assembly for Deinococcus grandis ATCC 43672	complete	GCA_009177165	57498.6	8114091940	57498	73.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1532	D.grandis 16S rRNA gene	Y11329	1467		57498

GC content

1532

GC-content (mol%)68.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM148543v1 assembly for Deinococcus grandis ATCC 43672
BV-BRC: 57498.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	98.11	no
125439	gram_stain	BacteriaNetⓘ	positive	99.69	no
125439	motility	BacteriaNetⓘ	no	97.36	no
125439	spore_formation	BacteriaNetⓘ	yes	96.16	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Deinococcus grandis ATCC 43672
NCBI: GCA_009177165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	52.05	no
125438	anaerobic	anaerobicⓘ	no	95.43	no
125438	aerobic	aerobicⓘ	yes	80.99	no
125438	spore-forming	spore-formingⓘ	no	67.72	no
125438	thermophilic	thermophileⓘ	no	93.31	yes
125438	flagellated	motile2+ⓘ	no	68.89	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers.	Theodorakopoulos N, Bachar D, Christen R, Alain K, Chapon V.	Microbiologyopen	10.1002/mbo3.119	2013
Genetics	Effects of heterologous genome microinjection on the enlargement of Enterococcus faecalis protoplasts.	Takahashi S, Nishida H.	Curr Res Microb Sci	10.1016/j.crmicr.2022.100104	2022
	The Conformation of the N-Terminal Tails of Deinococcus grandis Dps Is Modulated by the Ionic Strength.	Guerra JPL, Blanchet CE, Vieira BJC, Almeida AV, Waerenborgh JC, Jones NC, Hoffmann SV, Tavares P, Pereira AS.	Int J Mol Sci	10.3390/ijms23094871	2022
	Sensitivity of Deinococcus grandis rodZ deletion mutant to calcium ions results in enhanced spheroplast size.	Morita Y, Okumura M, Narumi I, Nishida H.	AIMS Microbiol	10.3934/microbiol.2019.2.176	2019
	Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan.	Satoh K, Onodera T, Omoso K, Takeda-Yano K, Katayama T, Oono Y, Narumi I.	Genome Announc	10.1128/genomea.01631-15	2016
	Evolution of Phage Tail Sheath Protein.	Evseev P, Shneider M, Miroshnikov K.	Viruses	10.3390/v14061148	2022
	A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae.	Zimmerman JM, Battista JR.	BMC Microbiol	10.1186/1471-2180-5-17	2005
Metabolism	Bacteria mediate methylation of iodine in marine and terrestrial environments.	Amachi S, Kamagata Y, Kanagawa T, Muramatsu Y.	Appl Environ Microbiol	10.1128/aem.67.6.2718-2722.2001	2001
Genetics	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
Genetics	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
Phylogeny	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
Phylogeny	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
Phylogeny	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
Phylogeny	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
Phylogeny	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
Phylogeny	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
Phylogeny	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

References

#1532	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3963
#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Deinococcus grandis (DSM 3963, ATCC 43672, IAM 13005)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001485435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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