Name: Deinococcus irradiatisoli 17bor-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159760

Type strain:

Species: Deinococcus irradiatisoli

Strain Designation: 17bor-2

Culture col. no.: KCTC 33907, NBRC 113037

Strain history: <- Myung Kyum, Kim, Seoul Womens Univ.

NCBI tax ID(s): 2202254 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Deinococcus irradiatisoli 17bor-2 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from soil sample irradiated by a 3 kGy gamma ray using a cobalt-60 gamma irradiator.

coccus-shaped
colony-forming
Gram-negative
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 irradiatisoli**
	Full Scientific Name (LPSN)	Deinococcus irradiatisoli Kim et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66692]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %98.7

[Ref.: #66692]	Cell shape	coccus-shaped

[Ref.: #66692]	Motility	no

[Ref.: #66692]	Colony color	pink to red
[Ref.: #66692]	Colony shape	circular

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

tryptic soy agar (TSA)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) agar

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

		Temperature
[Ref.: #66692]	growth	18-37 °C
[Ref.: #66692]	optimum	28-30 °C
[Ref.: #67771]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #66692]			optimum	6.5-7.5
[Ref.: #66692]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66692]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %98.8

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66692]		NaCl		growth	0-1	%(w/v)
[Ref.: #66692]		NaCl		optimum	0	%(w/v)

[Ref.: #66692]	Observation	The strain has resistance to gamma radiation.
[Ref.: #67771]	Observation	quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66692]	adipate ChEBI	-	assimilation
[Ref.: #66692]	casein	+	hydrolysis
[Ref.: #66692]	D-glucose ChEBI	+	assimilation
[Ref.: #66692]	D-mannitol ChEBI	-	assimilation
[Ref.: #66692]	D-mannose ChEBI	-	assimilation
[Ref.: #66692]	decanoate ChEBI	-	assimilation
[Ref.: #66692]	esculin ChEBI	+	hydrolysis
[Ref.: #66692]	gelatin ChEBI	-	hydrolysis
[Ref.: #66692]	L-arabinose ChEBI	-	assimilation
[Ref.: #66692]	malate ChEBI	-	assimilation
[Ref.: #66692]	maltose ChEBI	-	assimilation
[Ref.: #66692]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #66692]	nitrate ChEBI	-	reduction
[Ref.: #66692]	phenylacetate ChEBI	-	assimilation
[Ref.: #66692]	potassium gluconate ChEBI	-	assimilation
[Ref.: #66692]	sodium citrate ChEBI	-	assimilation
[Ref.: #66692]	starch ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #66692]	acetoin ChEBI	yes
[Ref.: #66692]	hydrogen sulfide ChEBI	no
[Ref.: #66692]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #66692]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #66692]	acid phosphatase	+	3.1.3.2
[Ref.: #66692]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66692]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #66692]	alpha-fucosidase	+	3.2.1.51
[Ref.: #66692]	alpha-galactosidase	+	3.2.1.22
[Ref.: #66692]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66692]	alpha-mannosidase	+	3.2.1.24
[Ref.: #66692]	arginine dihydrolase	+	3.5.3.6
[Ref.: #66692]	beta-galactosidase	+	3.2.1.23
[Ref.: #66692]	beta-glucosidase	+	3.2.1.21
[Ref.: #66692]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66692]	catalase	+	1.11.1.6
[Ref.: #66692]	cystine arylamidase	+	3.4.11.3
[Ref.: #66692]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66692]	esterase (C 4)	+
[Ref.: #66692]	esterase Lipase (C 8)	+
[Ref.: #66692]	leucine arylamidase	+	3.4.11.1
[Ref.: #66692]	lipase (C 14)	-
[Ref.: #66692]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66692]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66692]	trypsin	+	3.4.21.4
[Ref.: #66692]	urease	+	3.5.1.5
[Ref.: #66692]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66692]

Fatty acid	Percentage
C16:1 w7c and/or C16:1 w6c	18.7
C16:0	12.2
Cyclo-C17:0	9.9
C17:0	8.6
C15:0 anteiso	7.3
C15:1 w6c	4.1
C17:1 iso w5c	3.9
C16:0 iso	3.9
C17:0 anteiso	3.5
C18:0 iso	3.1
C17:0 iso	2.6
C17:1 w7c	2.6
C14:1 w5c	2.3
C19:0 iso	1.8
C16:1 5c	1.8
C15:1 iso H and/or C13:0 3OH	1

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

[Ref.: #66692]	Sample type/isolated from	soil sample irradiated by a 3 kGy gamma ray using a cobalt-60 gamma irradiator
[Ref.: #66692]	Geographic location (country and/or sea, region)	Nowongu
[Ref.: #66692]	Country	Republic of Korea
[Ref.: #66692]	Country ISO 3 Code	KOR
[Ref.: #66692]	Continent	Asia
[Ref.: #66692]	Geographic location	37.6280°/127.0900°
[Ref.: #66692]	Enrichment culture	R2A
[Ref.: #66692]	Enrichment culture duration	3 days
[Ref.: #66692]	Enrichment culture temperature	25 ̊C
[Ref.: #66692]	Isolation/enrichment procedure	standard dilution plating technique

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Hwarangno, Nowon, Seoul
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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.: #66692]	Deinococcus irradiatisoli strain 17bor-2 16S ribosomal RNA gene, partial sequence	KY939573	1444	GenBank ENA	2202254 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Deinococcus irradiatisoli 17bor-2	GCA_003173015	complete	GenBank ENA	2202254 tax ID	*

[Ref.: #66692]	GC-content	62.8 mol%	real time PCR (RTD-PCR)
[Ref.: #67771]	GC-content	62.8 mol%

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 irradiatisoli 17bor-2 NCBI: GCA_003173015.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	69.307	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	86.991	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	75.658	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	75.402	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	84.979	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.007	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Deinococcus irradiatisoli 17bor-2 NCBI: GCA_003173015
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	83.5

Availability in culture collections External links

[Ref.: #66692]

Culture collection no.

KCTC 33907, NBRC 113037

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil.	Kim DU, Jang JH, Kang MS, Kim JY, Zhang J, Lim S, Kim MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002968	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 )

#66692

Dong-Uk Kim, Jun Hwee Jang, Myung-Suk Kang, Ju-Young Kim, Jing Zhang, Sangyong Lim, Myung Kyum Kim: Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil. IJSEM 68: 3232 - 3236 2018 ( DOI 10.1099/ijsem.0.002968 , PubMed 30129916 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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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