Name: Isoptericola dokdonensis DS-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 138458

Type strain:

Species: Isoptericola dokdonensis

Strain Designation: DS-3

Culture col. no.: CIP 108921, KCTC 19128, JCM 15137

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-3

NCBI tax ID(s): 372663 (species)

SI-ID 297246

CIP 108921, KCTC 19128, JCM 15137

Special Collections

Section

When using BacDive for research please cite our paper

Isoptericola dokdonensis DS-3 is an aerobe, mesophilic, Gram-positive bacterium of the family Promicromonosporaceae.

Gram-positive
aerobe
mesophilic
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Promicromonosporaceae*
	Genus	*Isoptericola*
	Species	**Isoptericola dokdonensis**
	Full Scientific Name (LPSN)	Isoptericola dokdonensis Yoon et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #39794]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %94.03
[Ref.: #125439]	Gram stain	positive Confidence in %99.9

[Ref.: #39794]	Cell shape	coccus-shaped

[Ref.: #39794]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %93.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #39794]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #39794]

Culture medium growth

[Ref.: #39794]

Culture medium composition

expand / minimize

[Ref.: #39794]

Culture medium

CIP Medium 72

[Ref.: #39794]

Culture medium growth

[Ref.: #39794]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #39794]	growth	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.4

[Ref.: #67770]

Observation

quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #39794]	nitrate ChEBI	+	reduction
[Ref.: #39794]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #39794]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #39794]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #39794]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #39794]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #39794]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #39794]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #39794]	11423	not determinedn.d.	+	-	-	+	-	+	-	-	+/-	+	+	+	+	-	+/-	-	-	-	-	-	-	-	+/-	+	+	+	+	+	+/-	-	+	+	-	-	-	+	+	-	+	+	-	-	-	-	-	-	+	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #39794]	11550	-	+	+	+	+	+	-	-	-	-	+	+	+	+	-	+	+	+	-	-

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

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #39794]	Sample type/isolated from	Environment, Soil
[Ref.: #39794]	Geographic location (country and/or sea, region)	Dokdo Island
[Ref.: #39794]	Country	Republic of Korea
[Ref.: #39794]	Country ISO 3 Code	KOR
[Ref.: #39794]	Continent	Asia
[Ref.: #39794]	Isolation date	2004

[Ref.: #39794]	Geographic location (country and/or sea, region)	Dokdo island
[Ref.: #39794]	Country	Republic of Korea
[Ref.: #39794]	Country ISO 3 Code	KOR
[Ref.: #39794]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence DQ387860 (>99% sequence identity) for Isoptericola from Microbeatlas

Aquatic Samples	31
Soil Samples	82
Animal Samples	53
Plant Samples	29
Total Samples	195

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #39794]

Biosafety level

Risk group (French classification)

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.: #67771]	Isoptericola dokdonensis strain DS-3 16S ribosomal RNA gene, partial sequence	DQ387860	1474	GenBank ENA	372663 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Isoptericola dokdonensis DS-3	GCA_001636295	complete	GenBank ENA	1300344 tax ID	*
[Ref.: #66792]	Isoptericola dokdonensis DS-3	1300344.3	complete	PATRIC	1300344 tax ID	*
[Ref.: #66792]	Isoptericola dokdonensis DS-3	2687453494	complete	JGI IMG/M	1300344 tax ID	*

[Ref.: #67770]

GC-content

74.1 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: Isoptericola dokdonensis DS-3 DS-3 NCBI: GCA_001636295.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	94.03	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.339	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	80.844	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	62.686	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.775	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	93.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Isoptericola dokdonensis DS-3 PATRIC: 1300344.3
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	65.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	87.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.4

Availability in culture collections External links

[Ref.: #39794]

Culture collection no.

CIP 108921, KCTC 19128, JCM 15137

[Ref.: #95181]

SI-ID 297246

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isoptericola jiangsuensis sp. nov., a chitin-degrading bacterium.	Wu Y, Li WJ, Tian W, Zhang LP, Xu L, Shen QR, Shen B	Int J Syst Evol Microbiol	10.1099/ijs.0.012864-0	2009	*
Phylogeny	Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola.	Bae Y, Lee S, Kim K, Lee HK, Kwon SK, Kim JF	J Microbiol	10.1007/s12275-021-1452-6	2021	*
Phylogeny	Isoptericola dokdonensis sp. nov., isolated from soil.	Yoon JH, Schumann P, Kang SJ, Jung SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64430-0	2006	*

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 )

#39794 Collection of Institut Pasteur ; Curators of the CIP; CIP 108921

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

#68371

Automatically annotated from API 50CH acid .

#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 .

#95181

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297246.1 )

#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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Isoptericola dokdonensis DS-3 DS-3

Isoptericola dokdonensis DS-3

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