Name: Gordonia desulfuricans 213E
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10602

Type strain:

Species: Gordonia desulfuricans

Strain Designation: 213E

Culture col. no.: DSM 44462, CIP 109045, JCM 11762, NCIMB 40816, BCRC 16388, IFM 10355, KCTC 9941, NBRC 100010

Strain history: CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain 213E

NCBI tax ID(s): 1223540 (strain), 89051 (species)

SI-ID 50635

DSM 44462, NCIMB 40816, KCTC 9941, JCM 11762, NBRC 100010, BCRC 16388, CCRC 16388, CIP 109045

Section

Gordonia desulfuricans 213E is a mesophilic bacterium that was isolated from soil.

mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Gordoniaceae*
	Genus	*Gordonia*
	Species	**Gordonia desulfuricans**
	Full Scientific Name (LPSN)	Gordonia desulfuricans Kim et al. 1999

Information on morphological and physiological properties Morphology

[Ref.: #20060]	Colony color	Salmon orange (2012)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 2

[Ref.: #20060]	Colony color	Ivory (1014)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 3

[Ref.: #20060]	Colony color	Beige (1001)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 4

[Ref.: #20060]	Colony color	Beige (1001)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 5

[Ref.: #20060]	Colony color	Beige (1001)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 6

[Ref.: #20060]	Colony color	Beige (1001)
[Ref.: #20060]	Incubation period	10-14 days
[Ref.: #20060]	Cultivation medium used	ISP 7

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 2

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 3

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 4

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 5

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 6

[Ref.: #20060]	Multicellular complex forming ability	no
[Ref.: #20060]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11789]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #11789]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #11789]

Culture medium composition

expand / minimize

[Ref.: #20060]

Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 5

[Ref.: #20060]

Culture medium growth

[Ref.: #20060]

Culture medium composition

expand / minimize

[Ref.: #20060]

Culture medium

ISP 6

[Ref.: #20060]

Culture medium growth

[Ref.: #20060]

Culture medium composition

expand / minimize

[Ref.: #20060]

Culture medium

ISP 7

[Ref.: #20060]

Culture medium growth

[Ref.: #20060]

Culture medium composition

expand / minimize

[Ref.: #36504]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #36504]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #118919]

Culture medium

CIP Medium 72

[Ref.: #118919]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #11789]	growth	28 °C
[Ref.: #20060]	optimum	30 °C
[Ref.: #36504]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #11789]	Temperature range	mesophilic
[Ref.: #20060]	Temperature range	mesophilic
[Ref.: #36504]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20060]	arabinose ChEBI	+
[Ref.: #20060]	cellulose ChEBI	+
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #20060]	fructose ChEBI	+
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #20060]	glucose ChEBI	+
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #20060]	mannitol ChEBI	+
[Ref.: #20060]	myo-inositol ChEBI	-
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #20060]	raffinose ChEBI	-
[Ref.: #20060]	rhamnose ChEBI	+
[Ref.: #20060]	sucrose ChEBI	+
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #20060]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, 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.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	+	3.2.1.23	* from API Coryne, API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, 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.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #20060]	411	-	-	+	+	-	+	+	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	+	-	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.: #20060]	842	not determinedn.d.	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #11789]	Sample type/isolated from	soil
[Ref.: #11789]	Geographic location (country and/or sea, region)	Scotland, West Lothian, West Calder
[Ref.: #11789]	Country	United Kingdom
[Ref.: #11789]	Country ISO 3 Code	GBR
[Ref.: #11789]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	West Lothian, Scotland
[Ref.: #67770]	Country	United Kingdom
[Ref.: #67770]	Country ISO 3 Code	GBR
[Ref.: #67770]	Continent	Europe

[Ref.: #118919]	Sample type/isolated from	Environment, Soil
[Ref.: #118919]	Country	United Kingdom
[Ref.: #118919]	Country ISO 3 Code	GBR
[Ref.: #118919]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF101416 (>99% sequence identity) for Gordonia desulfuricans from Microbeatlas

Aquatic Samples	143
Soil Samples	73
Animal Samples	351
Plant Samples	16
Total Samples	583

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

[Ref.: #11789]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #20060]	Biosafety level	1	German classification
[Ref.: #118919]	Biosafety level	1	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.: #11789]	Gordonia desulfuricans strain 213E 16S ribosomal RNA gene, partial sequence	AF101416	1512	ENA	89051 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Gordonia desulfuricans NBRC 100010	GCA_001485495	contig	GenBank	1223540 tax ID
[Ref.: #66792]	Gordonia desulfuricans 213E	GCA_010119475	contig	GenBank	89051 tax ID	*
[Ref.: #66792]	Gordonia desulfuricans NBRC 100010	1223540.3	wgs	PATRIC	1223540 tax ID	*
[Ref.: #66792]	Gordonia desulfuricans NBRC 100010	2731957553	draft	JGI IMG/M	1223540 tax ID	*

[Ref.: #11789]	GC-content	64.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	63.7-64.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	68.1 mol%	genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonia desulfuricans NBRC 100010 PATRIC: 1223540.3
[Ref.: #69480]	motile	no	95.445	no
[Ref.: #69480]	gram-positive	yes	87.122	no
[Ref.: #69480]	anaerobic	no	99.108	no
[Ref.: #69480]	aerobic	yes	79.676	no
[Ref.: #69480]	halophile	no	92.539	no
[Ref.: #69480]	spore-forming	no	81.732	no
[Ref.: #69480]	thermophile	no	98.868	yes
[Ref.: #69480]	glucose-util	yes	89.112	yes
[Ref.: #69480]	flagellated	no	98.29	no
[Ref.: #69480]	glucose-ferment	no	87.71	yes

Availability in culture collections External links

[Ref.: #11789]

Culture collection no.

DSM 44462, CIP 109045, JCM 11762, NCIMB 40816, BCRC 16388, IFM 10355, KCTC 9941, NBRC 100010

[Ref.: #79876]

SI-ID 50635

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Biological devulcanization of ground natural rubber by Gordonia desulfuricans DSM 44462(T) strain.	Tatangelo V, Mangili I, Caracino P, Anzano M, Najmi Z, Bestetti G, Collina E, Franzetti A, Lasagni M	Appl Microbiol Biotechnol	10.1007/s00253-016-7691-5	2016	*
Phylogeny	Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.	Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M	Int J Syst Evol Microbiol	10.1099/00207713-50-6-2031	2000	*
Phylogeny	Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete.	Kim SB, Brown R, Oldfield C, Gilbert SC, Goodfellow M	Int J Syst Bacteriol	10.1099/00207713-49-4-1845	1999	*

References

#11789

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44462

#20060

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#36504 ; Curators of the CIP;

#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;

#68379

Automatically annotated from API Coryne .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#79876

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-ID50635.1 )

#118919 Collection of Institut Pasteur ; Curators of the CIP; CIP 109045
* These data were automatically processed and therefore are not curated

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Gordonia desulfuricans NBRC 100010

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