Deinococcus rufus (KCTC 33913, CCTCC AB 2017081, W37)

Name: Deinococcus rufus (KCTC 33913, CCTCC AB 2017081, W37)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158723

Type strain

Strain Designation W37

Culture col. no. KCTC 33913 CCTCC AB 2017081 W37

NCBI tax ID(s) 2136097

Special Collections KCTC Literature strains

History KCTC <- Qian Wang and Choi lina, Huzhong Agricultural Univ.

Links

Deinococcus rufus W37 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil near an iron factory in Busan.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 25197

KCTC 33913

@ref 20215

Last LPSN update 2026-05-29 08:44:01

Domain Bacteria

Phylum Deinococcota

Class Deinococci

Order Deinococcales

Family Deinococcaceae

Genus Deinococcus

Species Deinococcus rufus

Full scientific name Deinococcus rufus Wang et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65470	negative	1.5-1.6 µm	0.5-0.6 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative				93.82

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
65470	reddish	circular	3 days	ISP 2 medium

Culture and growth conditions

Culture medium

@ref	Name	Growth
65470	ISP 2 medium
65470	Reasoner's 2A agar
65470	ISP 2 agar
65470	NA agar
65470	1/10 trypton soy agar
65470	LB (Luria-Bertani) MEDIUM

Culture temp

@ref	Growth	Type	Temperature (°C)
65470	positive	optimum	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH
65470	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65470	aerobe
67771	aerobe
125439	facultative anaerobe	91.305

Spore formation

@ref	Spore formation	Confidence
125439		99.374

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65470	NaCl	positive	optimum	0-1 %

Observation

@ref	Observation
65470	Flagella are not been observed by SEM and TEM
65470	major polar lipids are an unidentified phosphoglycolipid, an unidentified aminophospholipid, four unidentified glycolipids, two unidentified phospholipids and an unidentified lipid
65470	menaquinone MK-8 is the predominant quinine
67771	quinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65470	16193 ChEBI	3-hydroxybenzoate	-	growth
65470	37054 ChEBI	3-hydroxybutyrate	+	growth
65470	58143 ChEBI	5-dehydro-D-gluconate	-	growth
65470	17128 ChEBI	adipate	-	growth
65470	17057 ChEBI	cellobiose	+	growth
65470	62968 ChEBI	cellulose	-	hydrolysis
65470	15824 ChEBI	D-fructose	+	growth
65470	12936 ChEBI	D-galactose	+	growth
65470	17634 ChEBI	D-glucose	+	growth
65470	16988 ChEBI	D-ribose	+	growth
65470	17924 ChEBI	D-sorbitol	+	growth
65470	65327 ChEBI	D-xylose	+	growth
65470	27689 ChEBI	decanoate	-	growth
65470	5291 ChEBI	gelatin	+	assimilation
65470	28087 ChEBI	glycogen	+	growth
65470	16087 ChEBI	isocitrate	-	growth
65470	16977 ChEBI	L-alanine	-	growth
65470	30849 ChEBI	L-arabinose	+	growth
65470	18287 ChEBI	L-fucose	+	growth
65470	15971 ChEBI	L-histidine	-	growth
65470	15589 ChEBI	L-malate	-	growth
65470	62345 ChEBI	L-rhamnose	+	growth
65470	17115 ChEBI	L-serine	+	growth
65470	24996 ChEBI	lactate	-	growth
65470	24996 ChEBI	lactate	+	growth
65470	17306 ChEBI	maltose	+	growth
65470	29864 ChEBI	mannitol	+	growth
65470	37684 ChEBI	mannose	+	growth
65470	17268 ChEBI	myo-inositol	+	growth
65470	506227 ChEBI	N-acetylglucosamine	+	growth
65470	17632 ChEBI	nitrate	-	reduction
65470	28044 ChEBI	phenylalanine	-	hydrolysis
65470	17814 ChEBI	salicin	+	growth
65470	30762 ChEBI	salicylate	+	growth
65470	32954 ChEBI	sodium acetate	-	growth
65470	53258 ChEBI	sodium citrate	-	growth
65470	28017 ChEBI	starch	-	hydrolysis
65470	9300 ChEBI	suberic acid	-	growth
65470	30031 ChEBI	succinate	-	growth
65470	17992 ChEBI	sucrose	+	growth
65470	53424 ChEBI	tween 20	-	hydrolysis
65470	53423 ChEBI	tween 40	-	hydrolysis
65470	53425 ChEBI	tween 60	-	hydrolysis
65470	53426 ChEBI	tween 80	-	hydrolysis
65470	18186 ChEBI	tyrosine	-	hydrolysis
65470	31011 ChEBI	valerate	-	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65470	15138 ChEBI	sulfide

Enzymes

@ref	Value	Activity	Ec
65470	acid phosphatase	+	3.1.3.2
65470	alpha-chymotrypsin	-	3.4.21.1
65470	alpha-fucosidase	-	3.2.1.51
65470	alpha-galactosidase	-	3.2.1.22
65470	alpha-glucosidase	+	3.2.1.20
65470	alpha-mannosidase	-	3.2.1.24
65470	arginine dihydrolase	+	3.5.3.6
65470	beta-galactosidase	+	3.2.1.23
65470	beta-glucosidase	+	3.2.1.21
65470	beta-glucuronidase	-	3.2.1.31
65470	catalase	+	1.11.1.6
65470	cytochrome oxidase	+	1.9.3.1
65470	esterase	+
65470	esterase Lipase (C 8)	+
65470	lipase	-
65470	naphthol-AS-BI-phosphohydrolase	+
65470	trypsin	-	3.4.21.4
65470	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65470

Fatty acid	Percentage
C16:1ω7c and/or C15:0 Iso 2OH	38.1
0,666666667	17.4
C17:1ω8c	9.3
C17:1 isoω9c	8.2
C17:0 iso	5
0,708333333	3.8
C16:1ω9c	3.6
C17:1ω6c	2.2
C18:1ω9c	1.8
0,625	1.7
C15:1ω6c	1.5
C18:1ω7c	1.5
C16:0 iso	0.9
C15:0 ISO	0.8
0,75	0.6
C17:0 anteiso	0.6
C17:1 anteisoω9c	0.6
C16:1 ISO H	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Heavy metal
#Engineered	#Industrial	#Plant (Factory)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Latitude	Longitude	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Geographic location	Country	Country ISO 3 Code	Continent
65470	soil near an iron factory in Busan	35.1641	128.976 35.1641/128.976	1 week	28	soil sample was diluted serially in saline solution (0.85 %, w/v), spread on Reasoner's 2A agar
67771	From wide-area sand district hang hole						Busan	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KY689943 (>99% sequence identity) for Deinococcus yunweiensis subclade from Microbeatlas

Aquatic Samples	375
Soil Samples	150
Animal Samples	788
Plant Samples	51
Total Samples	1364

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4264944v1 assembly for Deinococcus rufus CCTCC AB 2017081	scaffold	GCA_042649445	2136097	73.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65470	Deinococcus rufus 16S ribosomal RNA gene, partial sequence	KY689943
124043	Deinococcus rufus strain CCTCC AB 2017081 16S ribosomal RNA gene, partial sequence.	MT760259	1340		2136097

GC content

@ref	GC-content (mol%)
65470	69
67771	69.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4264944v1 assembly for Deinococcus rufus CCTCC AB 2017081
NCBI: GCA_042649445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	93.82	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.31	no
125439	motility	BacteriaNetⓘ	yes	71.45	no
125439	spore_formation	BacteriaNetⓘ	no	99.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinococcus rufus sp. nov., isolated from soil near an iron factory.	Wang Q, Song Y, Choi L, Liu H, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002724	2018

References

#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 )
#65470	Qian Wang, Yali Song, Lina Choi, Hongyu Liu, Gejiao Wang, Mingshun Li: Deinococcus rufus sp. nov., isolated from soil near an iron factory. IJSEM 68: 1622 - 1626 2018 ( DOI 10.1099/ijsem.0.002724 , PubMed 29561256 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 rufus (KCTC 33913, CCTCC AB 2017081, W37)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_042649445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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