Deinococcus reticulitermitis (DSM 25938, CGMCC 1.10218, NBRC 106334)

Name: Deinococcus reticulitermitis (DSM 25938, CGMCC 1.10218, NBRC 106334)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3899

Type strain

Strain Designation TM-1

Culture col. no. DSM 25938 CGMCC 1.10218 NBRC 106334 TM-1

NCBI tax ID(s) 856736

Special Collections DSMZ Literature strains

Links

Deinococcus reticulitermitis TM-1 is a mesophilic, Gram-negative, coccus-shaped prokaryote that was isolated from soil.

Gram-negative coccus-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398389

NBRC 106334,DSM 25938

@ref 20215

Last LPSN update 2025-12-16 09:47:40

Domain Thermotogati

Phylum Deinococcota

Class Deinococci

Order Deinococcales

Family Deinococcaceae

Genus Deinococcus

Species Deinococcus reticulitermitis

Full scientific name Deinococcus reticulitermitis Chen et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
29916	negative	1.0-2.0 µm	coccus-shaped

Pigmentation

29916

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18130	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: 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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18130	positive	growth	28	mesophilic
29916	positive	growth	20-40
29916	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29916	positive	optimum	6.0-7.0
29916	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Spore formation

29916

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29916	NaCl	positive	growth	0-1 %
29916	NaCl	positive	optimum	0-0.4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29916	4853 ChEBI	esculin	+	hydrolysis
29916	17306 ChEBI	maltose	+	carbon source
29916	37684 ChEBI	mannose	+	carbon source
29916	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
29916	catalase	+	1.11.1.6
29916	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	denitrification	100	2 of 2
66794	starch degradation	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	citric acid cycle	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	glycolysis	70.59	12 of 17
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	d-mannose degradation	66.67	6 of 9
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	NAD metabolism	66.67	12 of 18
66794	serine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	carotenoid biosynthesis	63.64	14 of 22
66794	proline metabolism	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	polyamine pathway	60.87	14 of 23
66794	gallate degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	glutathione metabolism	57.14	8 of 14
66794	cardiolipin biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	lipid metabolism	54.84	17 of 31
66794	d-xylose degradation	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	lysine metabolism	52.38	22 of 42
66794	chlorophyll metabolism	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	resorcinol degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	vitamin B1 metabolism	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	hydrogen production	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	3-phenylpropionate degradation	40	6 of 15
66794	vitamin K metabolism	40	2 of 5
66794	degradation of sugar alcohols	37.5	6 of 16
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	ascorbate metabolism	36.36	8 of 22
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	lipid A biosynthesis	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	carnitine metabolism	25	2 of 8
66794	biotin biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18130	soil	Wuhan, Hubei	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HM214546 (>99% sequence identity) for Deinococcus reticulitermitis subclade from Microbeatlas

Aquatic Samples	1724
Soil Samples	431
Animal Samples	3961
Plant Samples	386
Total Samples	6502

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18130	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
66792	IMG-taxon 2617270904 annotated assembly for Deinococcus reticulitermitis CGMCC 1.10218	scaffold	GCA_900109185	856736.3	2617270904	856736	65.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18130	Deinococcus reticulitermitis strain TM-1 16S ribosomal RNA gene, partial sequence	HM214546	1469		856736

GC content

18130

GC-content (mol%)65.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Deinococcus reticulitermitis CGMCC 1.10218
NCBI: GCA_900109185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.90	no
125439	motility	BacteriaNetⓘ	yes	58.00	no
125439	gram_stain	BacteriaNetⓘ	negative	84.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Deinococcus reticulitermitis CGMCC 1.10218
NCBI: GCA_900109185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	70.80	yes
125438	anaerobic	anaerobicⓘ	no	92.51	no
125438	aerobic	aerobicⓘ	yes	79.73	no
125438	spore-forming	spore-formingⓘ	no	76.10	yes
125438	thermophilic	thermophileⓘ	no	87.75	yes
125438	flagellated	motile2+ⓘ	no	77.91	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Mining and Characterization of Amylosucrase from Calidithermus terrae for Synthesis of alpha-Arbutin Using Sucrose.	Li A, He Y, Chen W, Tao H, Wu H, Li S.	Int J Mol Sci	10.3390/ijms252413359	2024
	Influence of the C-Terminal Tail of RecA Proteins from Alkaline pH-Resistant Bacterium Deinococcus Ficus.	Fan HF, Su S, Kuo YA, Chen CJ.	ACS Omega	10.1021/acsomega.0c02865	2020
Phylogeny	Deinococcus reticulitermitis sp. nov., isolated from a termite gut.	Chen W, Wang B, Hong H, Yang H, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.026567-0	2011

References

#18130	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25938
#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 )
#29916	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26287 (see below)
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 reticulitermitis (DSM 25938, CGMCC 1.10218, NBRC 106334)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900109185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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