Rhodococcus opacus (CIP 107348, R7)

Name: Rhodococcus opacus (CIP 107348, R7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 136650

Type strain

Strain Designation R7

Culture col. no. CIP 107348 R7

NCBI tax ID(s) 37919

Special Collections CIP

History 2002, G. Bestetti, Degli Studi di Milano Univ., Milano, Italy: strain R7 CIP <- 2002, G. Bestetti, Milano Univ., Milano, Italy: strain R7

Links

Rhodococcus opacus R7 is an obligate aerobe, Gram-positive, rod-shaped bacterium of the family Nocardiaceae.

Gram-positive rod-shaped obligate aerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 362149

CIP 107348

@ref 20215

Last LPSN update 2026-02-09 11:32:42

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus opacus

Full scientific name Rhodococcus opacus Klatte et al. 1995

Synonyms (2)

Rhodococcus percolatus
Rhodococcus imtechensis

BacDive ID	Other strains from **Rhodococcus opacus** (29)	Type strain
10998	R. opacus 1b, 18, DSM 43205, ATCC 51881, CIP 104549, ... (type strain)
10996	R. opacus DSM 1069
10997	R. opacus C125, DSM 8531
10999	R. opacus DSM 43206, ATCC 21499, DSM 441, CIP 104550, ...
11000	R. opacus DSM 43250, ATCC 51882
11001	R. opacus DSM 43251
11002	R. opacus Pellegrino 327, DSM 43252, CIP 104626
11003	R. opacus S676, 225, DSM 43280, ATCC 4275, IMET 7025, ...
11004	R. opacus 691-19, DSM 43943, IMET 7363
11005	R. opacus DSM 44072, CBS 330.61
11006	R. opacus DSM 44236
11007	R. opacus MoAcy1, DSM 44186
11008	R. opacus Tue Acy 1, DSM 44188
11010	R. opacus 305-97, L2aT3, PWD5, DSM 44304
11011	R. opacus 307-97, PWD7, S2aT5, S₂aT5, DSM ...
11012	R. opacus 310-97, L1aT1, PWD10, DSM 44307
11013	R. opacus GW-86a, DSM 44311
11014	R. opacus Bie-17, DSM 44312
11015	R. opacus 304-97, H1aT2, PWD4, DSM 44313
11016	R. opacus 315-97, PWD15, S1aT1, DSM 44314
11017	R. opacus 97-319, H3aT3, PWD19, DSM 44315
11018	R. opacus ISO-5, DSM 44600
11019	R. opacus ROL1, DSM 44853
11020	R. opacus ROL2, DSM 44854
11021	R. opacus R1L6, DSM 44855
11022	R. opacus DSM 46027, IMET 7365, NCIB 9702
103557	R. opacus ST033313(HKI),
160415	R. opacus 1CP, DSM 46757, VKM Ac-2638
173346	R. opacus GK 3, GK3, CIP 110889, CCMM B1295

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
125439	positive			94
36128	positive	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
36128	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36128	CIP Medium 72			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
36128	positive	growth	30
36128	positive	growth	10-30
36128	negative	growth	37
36128	negative	growth	41
36128	negative	growth	45

Physiology and metabolism

Oxygen tolerance

36128

Oxygen toleranceobligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
36128	NaCl	positive	growth	0-6 %
36128	NaCl		growth	8 %
36128	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
36128	16947 ChEBI	citrate	-	carbon source
36128	4853 ChEBI	esculin	-	hydrolysis
36128	606565 ChEBI	hippurate	+	hydrolysis
36128	17632 ChEBI	nitrate	-	reduction
36128	17632 ChEBI	nitrate	-	respiration
36128	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
36128	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
36128	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
36128	15688 ChEBI	acetoin	-
36128	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
36128	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
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
36128	amylase	-
36128	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
36128	caseinase	-	3.4.21.50
36128	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
36128	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
36128	gamma-glutamyltransferase	-	2.3.2.2
36128	gelatinase	-
36128	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
36128	lipase	-
68382	lipase (C 14)	-		from API zym
36128	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
36128	ornithine decarboxylase	-	4.1.1.17
36128	oxidase	-
36128	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
36128	tryptophan deaminase	-
36128	tween esterase	+
36128	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

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
36128	-	-	+	+	-	+	+	+	-	-	+	+	-	-	-	+	-	-	-	-

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
36128	not determinedn.d.	+	+	-	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	+	+	-	-	+	+	-	+	+	-	-	-	-	-	+	+	+	+	+	-	-	-	-	-	-	+	-	+	-	+	-	+	+	+	-	+	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	+	-	-	-	+	+	+	-	+	+	-	+	+	+	+	-	+	+	-	-	+	+	+	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
36128		Crespiatica Lodi	Italy	ITA	Europe
36128	Environment, Contaminated soil	Crespiatica Lodi	Italy	ITA	Europe	2000

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
36128	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM73643v1 assembly for Rhodococcus opacus R7	chromosome	GCA_000736435	37919.10	2609460172	37919	79.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus opacus strain R7
PATRIC: 37919.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	58.20	no
125439	motility	BacteriaNetⓘ	no	74.00	no
125439	gram_stain	BacteriaNetⓘ	positive	94.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus opacus strain R7
PATRIC: 37919.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.09	no
125438	anaerobic	anaerobicⓘ	no	97.72	yes
125438	spore-forming	spore-formingⓘ	yes	59.07	no
125438	aerobic	aerobicⓘ	yes	88.83	yes
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism.	Zampolli J, Collina E, Lasagni M, Di Gennaro P.	AMB Express	10.1186/s13568-014-0073-4	2014
Genetics	Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons.	Di Gennaro P, Zampolli J, Presti I, Cappelletti M, D'Ursi P, Orro A, Mezzelani A, Milanesi L	Genome Announc	10.1128/genomeA.00827-14	2014

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 )
#36128	Collection of Institut Pasteur ; Curators of the CIP; CIP 107348
#68382	Automatically annotated from API zym .
#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 )

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Rhodococcus opacus (CIP 107348, R7)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000736435

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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