Name: Gordonia rubripertincta DSM 43248
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 10561

Type strain:

Species: Gordonia rubripertincta

Culture col. no.: DSM 43248, ATCC 25593, CIP 100848, IMET 7372, NCTC 10668, CCUG 34958, LMG 5368, JCM 3199, BCRC 13381, BCRC 13697, CCM 2632, CCUG 12170, IFM 0147, JCM 3227, MTCC 698, NRRL B-16540, VKM Ac-1017

Strain history: CIP <- 1984, ATCC <- M. Tsukamura: strain 3605, Gordona rubra

NCBI tax ID(s): 36822 (species)

SI-ID 2982

LMG 5368, ATCC 25593, CCM 2632, CCUG 34958, DSM 43248, IMET 7372, JCM 3199, NCTC 10668, NRRL B-16540, CIP 100848, CCRC 13381, CCRC 13697, CCUG 12170, JCM 3227, VKM Ac-1017, BCRC 13381, BCRC 13697

Special Collections

Gordonia phage N13

Other strains from Gordonia rubripertincta

Section

When using BacDive for research please cite our paper

Gordonia rubripertincta DSM 43248 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

Gram-positive
rod-shaped
mesophilic
obligate aerobe
16S sequence
Bacteria

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	*Mycobacteriales*
	Family	*Gordoniaceae*
	Genus	*Gordonia*
	Species	**Gordonia rubripertincta**
	Full Scientific Name (LPSN)	Gordonia rubripertincta corrig. (Hefferan 1904) Stackebrandt et al. 1989

	Synonym	Gordonia rubropertinctus
	Synonym	Gordona rubripertincta
	Synonym	"Gordona* rubra"*
	Synonym	Rhodococcus rubropertinctus
	Synonym	Gordona rubropertinctus
	Synonym	Rhodococcus corallinus
	Synonym	"Bacillus* rubropertinctus"*
	Synonym	"Serratia* corallina"*

Information on morphological and physiological properties Morphology

[Ref.: #122293]	Gram stain	positive

[Ref.: #122293]	Cell shape	rod-shaped

[Ref.: #122293]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #10904]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #10904]

Culture medium growth

[Ref.: #10904]

Culture medium link

Medium recipe at MediaDive

[Ref.: #10904]

Culture medium composition

expand / minimize

[Ref.: #38434]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #38434]

Culture medium growth

[Ref.: #38434]

Culture medium composition

expand / minimize

[Ref.: #122293]

Culture medium

CIP Medium 3

[Ref.: #122293]

Culture medium growth

[Ref.: #122293]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #10904]		growth	37 °C
[Ref.: #38434]		growth	30 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #122293]		growth	25-45 °C
[Ref.: #122293]	no	growth	10 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122293]

Oxygen tolerance

obligate aerobe

[Ref.: #67770]

Observation

quinones: MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122293]	citrate ChEBI	-	carbon source
[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.: #122293]	esculin ChEBI	-	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[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.: #122293]	nitrate ChEBI	+	reduction
[Ref.: #122293]	nitrate ChEBI	-	respiration
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #122293]	nitrite ChEBI	-	reduction
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122293]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #122293]		acetoin ChEBI	-
[Ref.: #122293]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #122293]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[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, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #122293]	amylase	+
[Ref.: #122293]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #122293]	caseinase	-	3.4.21.50
[Ref.: #122293]	catalase	+	1.11.1.6
[Ref.: #122293]	DNase	-
[Ref.: #122293]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122293]	gelatinase	-
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #122293]	lecithinase	-
[Ref.: #122293]	lipase	-
[Ref.: #122293]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #122293]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122293]	oxidase	-
[Ref.: #122293]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #122293]	protease	-
[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.: #122293]	tween esterase	+
[Ref.: #122293]	urease	+	3.5.1.5
[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® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #122293]	53	not determinedn.d.	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	+	-	+

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.: #10904]	4406	+	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	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.: #10904]	14535	-	+	+/-	+/-	-	+/-	-	+/-	-	-	+/-	-	-	-	-	+	-	-	-	-
[Ref.: #122293]	6638	-	+	+	+	+	-	-	+	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #10904]	Sample type/isolated from	soil

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

[Ref.: #122293]	Sample type/isolated from	Environment, Soil
[Ref.: #122293]	Isolation date	1967
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY995557 (>99% sequence identity) for Gordonia from Microbeatlas

Aquatic Samples	44
Soil Samples	28
Animal Samples	117
Plant Samples	7
Total Samples	196

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

[Ref.: #10904]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122293]	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.: #20218]	Gordonia rubripertincta strain DSM 43248 16S ribosomal RNA gene, partial sequence	AY995557	1479	GenBank ENA	36822 tax ID	*
[Ref.: #20218]	Gordonia rubripertincta strain ATCC 25593 16S ribosomal RNA gene, partial sequence	GQ871822	610	GenBank ENA	36822 tax ID	*
[Ref.: #124043]	Gordonia rubripertincta strain JCM 3199 16S ribosomal RNA gene, partial sequence.	AY995558	1479	GenBank ENA	36822 tax ID	*

[Ref.: #67770]	GC-content	67 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	69 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #10904]

Culture collection no.

DSM 43248, ATCC 25593, CIP 100848, IMET 7372, NCTC 10668, CCUG 34958, LMG 5368, JCM 3199, BCRC 13381, BCRC 13697, CCM 2632, CCUG 12170, IFM 0147, JCM 3227, MTCC 698, NRRL B-16540, VKM Ac-1017

[Ref.: #79837]

SI-ID 2982


[Ref.: #124042]	Gordonia phage N13

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequences of Gordonia rubripertincta Bacteriophages AnarQue and Figliar.	Curran E, Callaway SE, Dumanlang RR, Harshaw AV, Palacio PN, Nakamura Y, Kimberley KW, Theoret JR, Yoon EJ, Windsor EJ, McKenna CC	Microbiol Resour Announc	10.1128/mra.01085-21	2022	*
Genetics	Genome Sequence of VanLee, a Singleton Actinobacteriophage That Infects Multiple Gordonia Strains.	Franco V, Barnhill K, Biggs A, Bland J, Choudhary H, Crogan T, Finocchiaro A, Fuller T, Hanwacker C, Howard Z, Iqbal M, Mathew A, Miller S, Padhye S, Rainey E, Rodriguez A, Stewart E, Chase M, Otero L, Pollenz RS	Microbiol Resour Announc	10.1128/MRA.00519-21	2021	*
Genetics	Genome Sequences of Gordonia Bacteriophages Jodelie19, BlingBling, and Burnsey.	Harrington DL, Barten HR, Audannio EI, Bragg FA, Garcia KA, Niswonger KM, MacAllister JR, McCarroll AM, O'Sullivan DM, Torres SE, Stanley CD, Yalzadeh D, Kimberley KW, McKenna CC, Theoret JR, Yoon EJ, Windsor EJ	Microbiol Resour Announc	10.1128/MRA.01280-20	2021	*
Genetics	Genome Sequences of Gordonia rubripertincta Bacteriophages Jellybones and NHagos.	Harrington DL, Stevens JL, Johnson MJ, Pochiro SJ, Moriarty MM, Robertson ME, Sanchez A, Whitby OG, Kimberley KW, McKenna CC, Theoret JR, Windsor EJ, Yoon EJ	Microbiol Resour Announc	10.1128/MRA.00935-20	2020	*
Genetics	Complete Genome Sequences of Genamy16 and NovaSharks, Two Gordonia rubripertincta Bacteriophages Isolated from Soil in Southeastern Florida.	Torruellas Garcia J, Ballarin S, Balusa N, Bell M, Caballero S, Chan J, Farez M, Guillen-Tapia A, Parent K, Pierre-Louis N, Polishuk V, Soni B, Subramanian S, Crump K	Microbiol Resour Announc	10.1128/mra.00973-22	2022	*
Genetics	Complete Genome Sequence of Gordonia rubripertincta Bacteriophage Hexbug Suggests Potential for a New CT Subcluster.	Barszczak DJ, Allison MJ, Cai Y, Forman L, Goldstein JM, Hakimjee SM, Scapicchio MT, Torres R, Gavin HE	Microbiol Resour Announc	10.1128/mra.00773-22	2022	*
Phylogeny	Genome Characteristics of Vardy, a Cluster DJ Actinobacteriophage Isolated on Gordonia rubripertincta in Western North Carolina.	Henson M, Fratarcangeli M, Park S, Minot A, Gainey MD	Microbiol Resour Announc	10.1128/mra.00704-22	2022	*
Genetics	Genome Sequence of CaiB, a DR Cluster Actinobacteriophage That Infects Gordonia rubripertincta.	Welsh B, Abdalla NM, Aldana E, Alvarado Fernandez VM, Arenales Salgado de Oliveira B, Fakhre D, Haymond AJ, Helton KM, Kanchibhatta A, Knight J, Marshall S, Martinez MLN, Merkher A, Morrow SE, Nguyen KP, Patel JJ, Patel SR, Rayala P, Ruiz-Houston KM, Satardekar AP, Shaikh SM, Terron Osorio AE, Weitz RC, Otero L, Pollenz RS	Microbiol Resour Announc	10.1128/mra.00376-22	2022	*

References

#10904

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43248

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#38434 ; Curators of the CIP;
#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 .

#79837

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-ID2982.1 )

#122293 Collection of Institut Pasteur ; Curators of the CIP; CIP 100848

#124042

Johannes Wittmann, Clara Rolland, Lorenz Reimer, Joaquim Sardà: PhageDive .

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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