Rhodococcus zopfii (DSM 44108, ATCC 51349, JCM 9919)

Name: Rhodococcus zopfii (DSM 44108, ATCC 51349, JCM 9919)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11024

Type strain

Strain Designation T-1

Culture col. no. DSM 44108 ATCC 51349 JCM 9919 CGMCC 4.1818 CIP 104275 7 more

NCBI tax ID(s) 1219030 43772

Special Collections DSMZ JCM KCTC CIP Wink compendium

History <- J. T. Staley, T1 ATCC 51349 <-- M. A. Stoecker T1 <-- R. P. Herwig. CIP <- 1994, R. Ruimy, CNRS, Villefranche/Mer, France <- ATCC <- M.A. Stoecker: strain T-1 <- R.P. Herwig

Links

Rhodococcus zopfii T-1 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from bioreactor.

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

Name and taxonomic classification

SI-ID 42941

MTCC 2572,ATCC 51349,JCM 9919,CIP 104275,DSM 44108,NCIMB 13393,KCTC 9812,NBRC 100606,KCTC 19218,CGMCC 4.1818,NRRL B-16942

@ref 20215

Last LPSN update 2026-02-09 11:20:25

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus zopfii

Full scientific name Rhodococcus zopfii Stoecker et al. 1994

BacDive ID	Other strains from **Rhodococcus zopfii** (2)	Type strain
11025	R. zopfii Tue Acy 3, DSM 44189
103562	R. zopfii ST033350(HKI),

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
124038	positive	rod-shaped
125438			92.5
125438	positive		91.466
125439			91.8
125439	positive		99.2

Colony morphology

@ref	Colony color	Incubation period	Medium used
19999	Pastel orange (2003)	10-14 days	ISP 2
19999		10-14 days	ISP 3
19999		10-14 days	ISP 4
19999		10-14 days	ISP 5
19999		10-14 days	ISP 6
19999		10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19999		ISP 2
19999		ISP 3
19999		ISP 4
19999		ISP 5
19999		ISP 6
19999		ISP 7

Multimedia

@ref:	11403
multimedia content:	DSM_44108.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44108.jpg
caption:	Medium 215 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11403	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11403	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19999	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19999	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19999	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19999	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19999	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19999	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
41082	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
124038	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11403	positive	growth	28
19999	positive	optimum	28
41082	positive	growth	30
67770	positive	growth	28
124038	positive	growth	25-41
124038	negative	growth	10
124038	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
124038	obligate aerobe
125439	obligate aerobe	99.2

Spore formation

19999

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19999	NaCl	positive	maximum	5 %
124038	NaCl	positive	growth	0-2 %
124038	NaCl		growth	4 %
124038	NaCl		growth	6 %
124038	NaCl		growth	8 %
124038	NaCl		growth	10 %

Observation

20216

ObservationDegrades toluene and other benzene derivatives

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19999	22599 ChEBI	arabinose	+
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
19999	62968 ChEBI	cellulose	+
124038	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
124038	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
19999	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
19999	17234 ChEBI	glucose	+
124038	17234 ChEBI	glucose	-	fermentation
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
124038	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
124038	17716 ChEBI	lactose	-	fermentation
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
19999	29864 ChEBI	mannitol	+
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
19999	17268 ChEBI	myo-inositol	+
124038	17632 ChEBI	nitrate	+	reduction
124038	17632 ChEBI	nitrate	-	respiration
124038	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
19999	16634 ChEBI	raffinose	+
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
19999	26546 ChEBI	rhamnose	+
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
124038	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
19999	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
19999	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
124038	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
124038	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
124038	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
124038	alcohol dehydrogenase	-	1.1.1.1
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
124038	amylase	-
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
124038	beta-galactosidase	-	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
124038	caseinase	-	3.4.21.50
124038	catalase	+	1.11.1.6
124038	DNase	-
68382	esterase lipase (C 8)	+		from API zym
124038	gamma-glutamyltransferase	-	2.3.2.2
124038	gelatinase	-
68368	gelatinase	-		from API 20E
124038	lecithinase	-
124038	lipase	-
68382	lipase (C 14)	-		from API zym
124038	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
124038	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
124038	oxidase	-
124038	phenylalanine ammonia-lyase	+	4.3.1.24
124038	protease	-
124038	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
124038	tween esterase	-
124038	urease	+	3.5.1.5
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
19999	+	+	+	-	+	-	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
19999	not determinedn.d.	+	-	+	-	+	+	+	+	-	+	-	-	-	-	-	+	-	-	-
124038	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
124038	not determinedn.d.	-	-	+/-	-	-	-	-	-	-	-	+	+	-	-	+/-	+/-	+/-	+/-	+/-	-	+/-	+/-	-	-	+	-	-	-	-	+/-	+/-	+/-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	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
124038	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	-	-	-	-	-	+	-	+	-	+	+	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11403	bioreactor	University Washington, Department of civil engeneering	USA	USA	North America
67770	Toluene-phenol bioreactor operated by the Department of Civil Engineering	University of Washington	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence X81934 (>99% sequence identity) for Rhodococcus from Microbeatlas

Aquatic Samples	349
Soil Samples	259
Animal Samples	272
Plant Samples	20
Total Samples	900

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11403	1	Risk group (German classification) According to TRBA 466
19999	1	German classification According to TRBA 466
124038	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM189502v1 assembly for Rhodococcus zopfii NBRC 100606 = JCM 9919	contig	GCA_001895025	1219030.8	2867071599	1219030	48.86
66792	ASM131370v1 assembly for Rhodococcus zopfii NBRC 100606 = JCM 9919	contig	GCA_001313705	1219030.9	2734481959	1219030
66792	ASM2213473v1 assembly for Rhodococcus zopfii ATCC 51349	contig	GCA_022134735	43772.6	8117065052	43772

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Rhodococcus zopfii 16S ribosomal RNA gene, partial sequence	AF191343	1478	43772
20218	R.zopfii 16S rRNA gene (ATCC 51349T)	X81934	1319	43772
124043	Rhodococcus zopfii strain DSM 44108 16S ribosomal RNA gene, partial sequence.	KF410350	1371	43772
124043	Rhodococcus zopfii strain ATCC 51349 16S ribosomal RNA gene, partial sequence.	MK775203	1306	43772
124043	Rhodococcus zopfii strain NBRC 100606(T) 16S ribosomal RNA gene, partial sequence.	MH236121	806	43772
124043	Rhodococcus zopfii strain NBRC 100606(T) 16S ribosomal RNA gene, partial sequence.	MH193361	706	43772

GC content

@ref	GC-content (mol%)	Method
11403	70
67770	70	thermal denaturation, midpoint method (Tm)
67770	68.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus zopfii NBRC 100606 = JCM 9919
NCBI: GCA_001313705

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	motility	BacteriaNetⓘ	no	91.80	no
125439	spore_formation	BacteriaNetⓘ	yes	69.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus zopfii NBRC 100606 = JCM 9919
PATRIC: 1219030.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.47	no
125438	anaerobic	anaerobicⓘ	no	97.53	yes
125438	spore-forming	spore-formingⓘ	no	63.51	yes
125438	aerobic	aerobicⓘ	yes	89.25	no
125438	thermophilic	thermophileⓘ	no	96.50	no
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	UV-LED Combined with Small Bioreactor Platform (SBP) for Degradation of 17alpha-Ethynylestradiol (EE2) at Very Short Hydraulic Retention Time.	Fradkin O, Mamane H, Kaplan A, Menashe O, Kurzbaum E, Betzalel Y, Avisar D.	Materials (Basel)	10.3390/ma14205960	2021
	LP-UV-Nano MgO₂ Pretreated Catalysis Followed by Small Bioreactor Platform Capsules Treatment for Superior Kinetic Degradation Performance of 17alpha-Ethynylestradiol.	Vaddadi LP, Avisar D, Vadivel VK, Menashe O, Kurzbaum E, Cohen-Yaniv V, Mamane H.	Materials (Basel)	10.3390/ma13010083	2019
Metabolism	Isolation, Characterization, and Degradation Performance of the 17beta-Estradiol-Degrading Bacterium Novosphingobium sp. E2S.	Li S, Liu J, Sun M, Ling W, Zhu X.	Int J Environ Res Public Health	10.3390/ijerph14020115	2017
Pathogenicity	Relationships between colony morphotypes and oil tolerance in Rhodococcus rhodochrous.	Iwabuchi N, Sunairi M, Anzai H, Nakajima M, Harayama S.	Appl Environ Microbiol	10.1128/aem.66.11.5073-5077.2000	2000
Phylogeny	Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources.	Rehfuss M, Urban J	Syst Appl Microbiol	10.1016/j.syapm.2005.05.011	2005
Phylogeny	Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm.	Jiang Y, Zheng C, Yu T, Li J, Ai J, Li M, Liu X, Deng Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005426	2022

References

#11403	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44108
#19999	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 )
#20216	Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) . Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI):
#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 )
#41082	; 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;
#68368	Automatically annotated from API 20E .
#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 .
#124038	Collection of Institut Pasteur ; Curators of the CIP; CIP 104275
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Rhodococcus zopfii (DSM 44108, ATCC 51349, JCM 9919)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001895025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media