Deinococcus depolymerans (DSM 27395, CCUG 53609, JCM 14368)

Name: Deinococcus depolymerans (DSM 27395, CCUG 53609, JCM 14368)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 22984

Type strain

Strain Designation TDMA-24

Culture col. no. DSM 27395 CCUG 53609 JCM 14368 NBRC 102115 TDMA-24

NCBI tax ID(s) 392408

Special Collections DSMZ CCUG JCM

History <- NBRC <- D. Asker, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; TDMA-24 D. Asker et al. TDMA-24.

Links

Deinococcus depolymerans TDMA-24 is a bacterium that was isolated from fresh water sample.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401960

NBRC 102115,JCM 14368,DSM 27395,CCUG 53609

@ref 20215

Last LPSN update 2026-02-09 11:23:38

Domain Bacteria

Phylum Deinococcota

Class Deinococci

Order Deinococcales

Family Deinococcaceae

Genus Deinococcus

Species Deinococcus depolymerans

Full scientific name Deinococcus depolymerans Asker et al. 2011

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19115	GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)		Medium recipe at MediaDive	Name: 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

@ref	Growth	Type	Temperature (°C)
19115	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Murein

@ref	Murein short key	Type
19115	A21.01	A3ß L-Orn-Gly₂_-₃

Observation

67770

Observationquinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68379	catalase	-	1.11.1.6	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
65638	-	-	+	+	-	+	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
65638	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19115	fresh water sample	Tottori, Misasa	Japan	JPN	Asia
67770	Freshwater sample collected at Misasa	Tottori Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB264134 (>99% sequence identity) for Deinococcus from Microbeatlas

Aquatic Samples	669
Soil Samples	40
Animal Samples	1437
Plant Samples	33
Total Samples	2179

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19115	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952202v1 assembly for Deinococcus depolymerans JCM 14368	scaffold	GCA_039522025	392408	70.31
124043	ASM3954495v1 assembly for Deinococcus depolymerans NBRC 102115	contig	GCA_039544955	392408	67.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19115	Deinococcus depolymerans gene for 16S rRNA, partial sequence, strain: TDMA-24	AB264134	1424		392408
124043	Deinococcus depolymerans strain JCM 14368 16S ribosomal RNA gene, partial sequence.	MT760361	1321		392408

GC content

@ref	GC-content (mol%)	Method
19115	70.5
67770	70.5-70.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
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 depolymerans sp. nov., a gamma- and UV-radiation-resistant bacterium, isolated from a naturally radioactive site.	Asker D, Awad TS, McLandsborough L, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.013482-0	2010
Phylogeny	Deinococcus taklimakanensis sp. nov., isolated from desert soil.	Liu Z, Kim MC, Wang L, Zhu G, Zhang Y, Huang Y, Wei Z, Danzeng W, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.002168	2017

References

#19115	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27395
#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 )
#65638	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53609
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 depolymerans (DSM 27395, CCUG 53609, JCM 14368)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Murein

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039522025

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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