Rhodococcus ruber (CIP 104640, CCUG 20988)

Name: Rhodococcus ruber (CIP 104640, CCUG 20988)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 136331

Type strain

Culture col. no. CIP 104640 CCUG 20988

NCBI tax ID(s) 1830

Special Collections CCUG CIP

History CIP <- 1995, CCUG <- 1987, M. Ridell/A. Lind <- 1976, NCIMB

Links

Rhodococcus ruber CIP 104640 is a microaerophile, mesophilic, Gram-positive prokaryote of the family Nocardiaceae.

Gram-positive rod-shaped microaerophile mesophilic

Name and taxonomic classification

SI-ID 56701

CCUG 20988,CIP 104640

@ref 20215

Last LPSN update 2025-12-16 10:02:32

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus ruber

Full scientific name Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)

Synonyms (2)

"Streptothrix rubra"
Rhodococcus electrodiphilus

BacDive ID	Other strains from **Rhodococcus ruber** (41)	Type strain
10927	R. ruber M-1, N361, A-0205, CCUG 51069, DSM 43338, ... (type strain)
10921	R. ruber An213, DSM 6264, IMET 7643
10922	R. ruber Sm-1, DSM 7511, ATCC 51239
10923	R. ruber Wrink, DSM 7512
10924	R. ruber Propb, DSM 8425
10925	R. ruber Pellegrino 327, DSM 43232, SN 5101
10926	R. ruber N324, DSM 43335, ATCC 15998, CCUG 23602, ...
10928	R. ruber Pellegrino 330, DSM 43560, SN 5102
10929	R. ruber DSM 43561, SN 5108
10930	R. ruber DSM 43562, SN 5109
10931	R. ruber DSM 43563, SN 5110
10932	R. ruber DSM 43564, SN 5202
10933	R. ruber DSM 43565, SN 5203
10934	R. ruber DSM 43566, SN 5204
10935	R. ruber DSM 43567, SN 5205
10936	R. ruber DSM 43571, CBS 245.53, SN 6000
10937	R. ruber 81 N grün, DSM 43588
10938	R. ruber 81 N Mo, DSM 43589
10939	R. ruber NI, N_I, DSM 43594
10940	R. ruber NIIa, N_I_I_a, ...
10941	R. ruber N453, DSM 43961
10942	R. ruber 219, DSM 44190
10943	R. ruber S679, ES3-T, FH2170, FERM-P 3374, DSM 44319, ...
10944	R. ruber CD4=CD+1-4II, CD4=CD⁺₁-4II, ...
10945	R. ruber CD4, DSM 44495
10946	R. ruber SM 1790, TB1, DSM 44539
10947	R. ruber EH1, SM1789, DSM 44540
10949	R. ruber ES 1-T, FERM-P 2882, DSM 44755, ATCC 31191, ...
10950	R. ruber DSM 44758
10951	R. ruber 373, N 123, DSM 46008, CBS 334.51, CCM 198, ...
10952	R. ruber 906B, Casenuovo, Inst. Sup, Gdf N325, Casenuovo, ...
10953	R. ruber McClung M-122, DSM 46043, CIP 104660, IMET ...
10954	R. ruber B113, DSM 46646, IMET 7358
10955	R. ruber Chol-4, DSM 45280
10956	R. ruber C208, DSM 45332
103875	R. ruber ST004516(HKI),
130482	R. ruber A5, DSM 46851, CECT 8556
130483	R. ruber EE1, DSM 46852, CECT 8555
130484	R. ruber EE6, DSM 46853, CECT 8612
136328	R. ruber CIP 104637, CCUG 23577, PCM 2171
151928	R. ruber CCUG 45236

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
35711	positive	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
35711	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
35711	CIP Medium 3			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
35711	positive	growth	30	mesophilic
35711	positive	growth	10-41
35711	negative	growth	45
47246	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
47246	microaerophile
35711	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
35711	NaCl	positive	growth	0-8 %
35711	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
35711	16947 ChEBI	citrate	+	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
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
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
35711	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
35711	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	62345 ChEBI	L-rhamnose	-	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
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	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
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
35711	17632 ChEBI	nitrate	+	reduction
35711	17632 ChEBI	nitrate	-	respiration
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
35711	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
35711	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
35711	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
35711	alcohol dehydrogenase	-	1.1.1.1
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
35711	amylase	-
35711	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
35711	caseinase	-	3.4.21.50
35711	catalase	+	1.11.1.6
68379	catalase	+	1.11.1.6	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
35711	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
35711	gamma-glutamyltransferase	-	2.3.2.2
35711	gelatinase	-
68379	gelatinase	-		from API Coryne
35711	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
35711	lipase	-
68382	lipase (C 14)	-		from API zym
35711	lysine decarboxylase	-	4.1.1.18
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
35711	ornithine decarboxylase	-	4.1.1.17
35711	oxidase	-
35711	phenylalanine ammonia-lyase	-	4.3.1.24
35711	protease	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
35711	tryptophan deaminase	-
35711	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@ref

47246

Fatty acid	Percentage	ECL
C16:0	33.6	16
C18:1 ω9c	20.7	17.769
C16:1 ω7c/C15:0 ISO 2OH	18	15.85
C18:2 ω6,9c/C18:0 ANTE	8.1	17.724
TBSA 10Me18:0	6.5	18.392
C16:1 ω7c	3	15.819
C14:0	2.6	14
C18:0	2.5	18
C15:0	2.3	15
C17:1 ω8c	1.4	16.792
C17:0	1.4	17

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
47246	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+

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
47246	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
35711	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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
35711	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
35711	not determinedn.d.	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	-	-	+	+	-	+	-	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	+	+	-

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
35711	1	Risk group (French classification)

Sequence information

Genome-based predictions

Literature

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 )
#35711	Collection of Institut Pasteur ; Curators of the CIP; CIP 104640
#47246	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 20988
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 ruber (CIP 104640, CCUG 20988)

Name and taxonomic classification