Name: Deinococcus ruber JSH3-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133314

Type strain:

Species: Deinococcus ruber

Strain Designation: JSH3-1

Culture col. no.: KCTC 33790, JCM 31311

Strain history: M. K. Kim; Dept. of Bio & Environ. Technol., Seoul Women's Univ., South Korea; JSH3-1.

NCBI tax ID(s): 1848197 (species)

Special Collections

Other strains from Deinococcus ruber

Section

When using BacDive for research please cite our paper

Deinococcus ruber JSH3-1 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from wet soil samples .

coccus-shaped
colony-forming
Gram-positive
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Deinococcota*
	Class	*Deinococci*
	Order	*Deinococcales*
	Family	*Deinococcaceae*
	Genus	*Deinococcus*
	Species	**Deinococcus ruber**
	Full Scientific Name (LPSN)	Deinococcus ruber Kim et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25145]	Gram stain	positive

[Ref.: #25145]	Cell length	2.0-2.5 µm

[Ref.: #25145]	Cell shape	coccus-shaped

[Ref.: #25145]	Motility	no

[Ref.: #25145]	Colony color	pale reddish
[Ref.: #25145]	Colony shape	circular
[Ref.: #25145]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25145]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25145]

Culture medium growth

		Temperature
[Ref.: #25145]	growth	4.0-37.0 °C
[Ref.: #25145]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #25145]			optimum	7
[Ref.: #25145]			growth	7.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25145]

Oxygen tolerance

aerobe

[Ref.: #25145]

Ability of spore formation

[Ref.: #67770]

Observation

quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25145]	(-)-quinic acid ChEBI	-	respiration
[Ref.: #25145]	(S)-lactate ChEBI	-	respiration
[Ref.: #25145]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25145]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #25145]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #25145]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25145]	3-O-methyl-D-glucose ChEBI	-	respiration
[Ref.: #25145]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #25145]	acetate ChEBI	-	respiration
[Ref.: #25145]	acetoacetate ChEBI	-	respiration
[Ref.: #25145]	alpha-D-glucose ChEBI	-	respiration
[Ref.: #25145]	alpha-lactose ChEBI	-	respiration
[Ref.: #25145]	bromosuccinate ChEBI	-	respiration
[Ref.: #25145]	cellobiose ChEBI	-	respiration
[Ref.: #25145]	citrate ChEBI	-	respiration
[Ref.: #25145]	D-arabitol ChEBI	-	respiration
[Ref.: #25145]	D-aspartate ChEBI	-	respiration
[Ref.: #25145]	D-fructose ChEBI	-	respiration
[Ref.: #25145]	D-fructose 6-phosphate ChEBI	+	respiration
[Ref.: #25145]	D-fucose ChEBI	-	respiration
[Ref.: #25145]	D-galactonic acid lactone ChEBI	-	respiration
[Ref.: #25145]	D-galactose ChEBI	-	respiration
[Ref.: #25145]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #25145]	D-glucarate ChEBI	-	respiration
[Ref.: #25145]	D-gluconate ChEBI	-	respiration
[Ref.: #25145]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #25145]	D-glucuronate ChEBI	-	respiration
[Ref.: #25145]	D-malate ChEBI	-	respiration
[Ref.: #25145]	D-mannitol ChEBI	-	respiration
[Ref.: #25145]	D-mannose ChEBI	-	respiration
[Ref.: #25145]	D-serine ChEBI	-	respiration
[Ref.: #25145]	D-sorbitol ChEBI	-	respiration
[Ref.: #25145]	dextrin ChEBI	-	respiration
[Ref.: #25145]	formate ChEBI	-	respiration
[Ref.: #25145]	galactarate ChEBI	-	respiration
[Ref.: #25145]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #25145]	gelatin ChEBI	-	respiration
[Ref.: #25145]	gentiobiose ChEBI	-	respiration
[Ref.: #25145]	glucuronamide ChEBI	+	respiration
[Ref.: #25145]	glycerol ChEBI	-	respiration
[Ref.: #25145]	glycine-proline ChEBI	-	respiration
[Ref.: #25145]	inosine ChEBI	-	respiration
[Ref.: #25145]	L-alanine ChEBI	-	respiration
[Ref.: #25145]	L-arginine ChEBI	-	respiration
[Ref.: #25145]	L-aspartate ChEBI	-	respiration
[Ref.: #25145]	L-fucose ChEBI	-	respiration
[Ref.: #25145]	L-glutamate ChEBI	-	respiration
[Ref.: #25145]	L-histidine ChEBI	-	respiration
[Ref.: #25145]	L-malate ChEBI	-	respiration
[Ref.: #25145]	L-pyroglutamic acid ChEBI	-	respiration
[Ref.: #25145]	L-rhamnose ChEBI	-	respiration
[Ref.: #25145]	L-serine ChEBI	-	respiration
[Ref.: #25145]	maltose ChEBI	-	respiration
[Ref.: #25145]	melibiose ChEBI	-	respiration
[Ref.: #25145]	methyl (R)-lactate ChEBI	-	respiration
[Ref.: #25145]	methyl beta-D-glucopyranoside ChEBI	-	respiration
[Ref.: #25145]	methyl pyruvate ChEBI	-	respiration
[Ref.: #25145]	myo-inositol ChEBI	-	respiration
[Ref.: #25145]	N-acetyl-D-mannosamine ChEBI	-	respiration
[Ref.: #25145]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #25145]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #25145]	n-acetylneuraminate ChEBI	-	respiration
[Ref.: #25145]	pectin ChEBI	-	respiration
[Ref.: #25145]	propionate ChEBI	-	respiration
[Ref.: #25145]	raffinose ChEBI	-	respiration
[Ref.: #25145]	salicin ChEBI	-	respiration
[Ref.: #25145]	stachyose ChEBI	-	respiration
[Ref.: #25145]	sucrose ChEBI	-	respiration
[Ref.: #25145]	trehalose ChEBI	-	respiration
[Ref.: #25145]	turanose ChEBI	-	respiration
[Ref.: #25145]	tween 40 ChEBI	-	respiration
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25145]		catalase	+	1.11.1.6
[Ref.: #25145]		cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #25145]	Sample type/isolated from	wet soil samples (garden soil)
[Ref.: #25145]	Geographic location (country and/or sea, region)	Noeun-myeon, Chungjusi, Chungcheongbuk-do
[Ref.: #25145]	Country	Republic of Korea
[Ref.: #25145]	Country ISO 3 Code	KOR
[Ref.: #25145]	Continent	Asia
[Ref.: #25145]	Geographic location	37.0000°/127.0000°
[Ref.: #25145]	Enrichment culture	R2A agar (Difco)
[Ref.: #25145]	Enrichment culture duration	7 days
[Ref.: #25145]	Enrichment culture temperature	25 ̊C
[Ref.: #25145]	Isolation/enrichment procedure	soil samples were irradiated with gamma radiation prior to isolation

[Ref.: #67770]	Sample type/isolated from	Garden soil
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Garden
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU865685 (>99% sequence identity) for Deinococcus ruber subclade from Microbeatlas

Aquatic Samples	359
Soil Samples	569
Animal Samples	338
Plant Samples	386
Total Samples	1652

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Deinococcus ruber strain JSH3-1 16S ribosomal RNA gene, partial sequence	KU865685	1434	GenBank ENA	1848197 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Deinococcus ruber JCM 31311	GCA_014648095	contig	GenBank ENA	1848197 tax ID	*
[Ref.: #66792]	Deinococcus ruber strain JCM 31311	1848197.3	wgs	PATRIC	1848197 tax ID	*

[Ref.: #67770]

GC-content

62 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Deinococcus ruber strain JCM 31311 PATRIC: 1848197.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	56.791	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.133	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	71.524	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.775	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	83.09	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	78.158	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Deinococcus ruber JCM 31311 NCBI: GCA_014648095
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	88
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	54.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	84.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative aerobe	78.2

Availability in culture collections External links

[Ref.: #25145]

Culture collection no.

KCTC 33790, JCM 31311

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil.	Kim EB, Kang MS, Joo ES, Jeon SH, Jeong SW, Lim SY, Jung HY, Srinivasan S, Kim MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.001567	2017	*

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 )

#25145

E. B. K. Kim, M. S.,Joo, E. S.,Jeon, S. H.,Jeong, S. W.,Lim, S. Y.,Jung, H. Y.,Srinivasan, S.,Kim, M. K.: Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil. IJSEM 67: 72 - 76 2017 ( DOI 10.1099/ijsem.0.001567 , PubMed 27902195 )

#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 .

* These data were automatically processed and therefore are not curated

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Deinococcus ruber strain JCM 31311

Deinococcus ruber JCM 31311

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