Rhodococcus coprophilus (DSM 43347, ATCC 29080, CUB 687)

Name: Rhodococcus coprophilus (DSM 43347, ATCC 29080, CUB 687)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10836

Type strain

Strain Designation N 744, A-0200, N744, 687

Culture col. no. DSM 43347 ATCC 29080 CUB 687 IMET 7375 JCM 3200 22 more

NCBI tax ID(s) 1219011 38310

Special Collections DSMZ CCUG JCM KCTC CIP Wink compendium

Links

Rhodococcus coprophilus N 744 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from lake mud.

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

Name and taxonomic classification

SI-ID 92420

LMG 5357,ATCC 29080,CCM 2723,IMET 47375,IMET 7375,JCM 3200,NCIB 11211,NCTC 10994,PCM 2174,NRRL B-16537,CCUG 23572,CIP 104178,NCIMB 11211,CCRC 13383,VKM Ac-571,CBS 313.75,KCTC 9804,CECT 5751,NBRC 100603,BCRC 13383,CGMCC 4.1813,DSM 43347,CCUG 51067

@ref 20215

Last LPSN update 2025-12-16 09:49:26

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus coprophilus

Full scientific name Rhodococcus coprophilus Rowbotham and Cross 1979 (Approved Lists 1980)

BacDive ID	Other strains from **Rhodococcus coprophilus** (10)	Type strain
10835	R. coprophilus N 650, DSM 43339, CIP 104628, CUB 628, CCUG ...
10837	R. coprophilus 34G12, DSM 43447
10838	R. coprophilus 81NKrauth, 81N_Krauth, DSM 43591
10839	R. coprophilus DSM 44751
10840	R. coprophilus A747 Lacey, DSM 46034, CIP 104657, CUB 415, ...
136330	R. coprophilus CIP 104639, CCUG 23571
144206	R. coprophilus CCUG 23605
145161	R. coprophilus CCUG 27780
159040	R. coprophilus WB03-B01-AE, DSM 105337
159041	R. coprophilus BL-253-APC-6A1W, DSM 106145

Morphology

Cell morphology

@ref	Gram stain	Cell shape
118743	positive	rod-shaped
125438
125439	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
10971	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
34042	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
118743	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
10971	positive	growth	28	mesophilic
18486	positive	optimum	28	mesophilic
34042	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
118743	positive	growth	10-45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
118743	obligate aerobe
125439	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
18486	NaCl	positive	maximum	5 %
118743	NaCl	positive	growth	0-4 %
118743	NaCl		growth	6 %
118743	NaCl		growth	8 %
118743	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
18486	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
18486	62968 ChEBI	cellulose	+
118743	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
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
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	16899 ChEBI	D-mannitol	-	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	17924 ChEBI	D-sorbitol	-	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
118743	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
18486	28757 ChEBI	fructose	+
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
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
18486	17234 ChEBI	glucose	+
118743	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
118743	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
118743	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
18486	29864 ChEBI	mannitol	+
68371	6731 ChEBI	melezitose	-	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
18486	17268 ChEBI	myo-inositol	+
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
118743	17632 ChEBI	nitrate	+	reduction
118743	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
18486	16634 ChEBI	raffinose	+
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
18486	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
118743	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
18486	17992 ChEBI	sucrose	+
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
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
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
18486	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
118743	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
118743	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-	from API 20E
118743	17234 ChEBI	glucose
68368	35581 ChEBI	indole		from API 20E

Enzymes

@ref	Value	Activity	Ec
118743	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-mannosidase	-	3.2.1.24	from API zym
118743	amylase	-
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
118743	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
118743	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118743	DNase	-
68382	esterase lipase (C 8)	+		from API zym
118743	gamma-glutamyltransferase	-	2.3.2.2
68368	gelatinase	-		from API 20E
118743	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118743	lipase	+
118743	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
118743	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
118743	oxidase	-
118743	phenylalanine ammonia-lyase	+	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
118743	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
118743	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	acetate fermentation	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methane metabolism	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	aspartate and asparagine metabolism	100	9 of 9
66794	octane oxidation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	citric acid cycle	92.86	13 of 14
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	pentose phosphate pathway	81.82	9 of 11
66794	lipoate biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	purine metabolism	76.6	72 of 94
66794	alanine metabolism	75.86	22 of 29
66794	lactate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	oxidative phosphorylation	73.63	67 of 91
66794	methionine metabolism	73.08	19 of 26
66794	metabolism of disaccharids	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	bile acid biosynthesis, neutral pathway	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	carotenoid biosynthesis	63.64	14 of 22
66794	tryptophan metabolism	63.16	24 of 38
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	pyrimidine metabolism	62.22	28 of 45
66794	sulfate reduction	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	allantoin degradation	55.56	5 of 9
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	carnitine metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	histidine metabolism	48.28	14 of 29
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	d-xylose degradation	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18

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
18486	-	-	-	-	-	-	-	-	-	-	-	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
18486	not determinedn.d.	-	-	+	-	+	+	-	-	-	+	-	-	-	-	+	-	-	-	-
118743	-	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
118743	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
118743	not determinedn.d.	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type
10971	lake mud
67770	Lake mud
118743	Environment, Lake mud

Taxonmaps

69479

Global distribution of 16S sequence X80626 (>99% sequence identity) for Rhodococcus coprophilus subclade from Microbeatlas

Aquatic Samples	548
Soil Samples	872
Animal Samples	511
Plant Samples	73
Total Samples	2004

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
10971	1	Risk group (German classification) According to TRBA 466
18486	1	German classification According to TRBA 466
118743	1	Risk group (French classification) According to TRBA 466

Phages

@ref	Name	Strain number
124042	Rhodococcus phage N36	DSM 43347

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	50618_D02 assembly for Rhodococcus coprophilus NCTC10994	complete	GCA_900478115	38310.3	2808606534	38310	98.32
67770	ASM189504v1 assembly for Rhodococcus coprophilus NBRC 100603	contig	GCA_001895045	1219011.3	2903948744	1219011	72.53

Genome browser: GCA_900478115

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	R.coprophilus 16S rRNA gene (ATCC 29080T)	X81928	1321	38310
20218	Rhodococcus coprophilus strain DSM 43347 16S ribosomal RNA gene, partial sequence	KF410348	1374	38310
20218	Rhodococcus coprophilus 16S rRNA gene, strain DSM43347T	X80626	1481	38310
20218	Rhodococcus coprophilus strain JCM 3200 16S ribosomal RNA gene, partial sequence	U93340	1481	38310

GC content

@ref	GC-content (mol%)
67770	60-64
67770	69.3
67770	66.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus coprophilus NCTC10994
NCBI: GCA_900478115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	motility	BacteriaNetⓘ	no	89.00	no
125439	spore_formation	BacteriaNetⓘ	yes	60.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus coprophilus NCTC10994
NCBI: GCA_900478115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.75	no
125438	anaerobic	anaerobicⓘ	no	98.92	yes
125438	aerobic	aerobicⓘ	yes	87.30	yes
125438	spore-forming	spore-formingⓘ	no	58.64	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Enzymology	Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR.	Laurent FJ, Provost F, Boiron P.	J Clin Microbiol	10.1128/jcm.37.1.99-102.1999	1999
Metabolism	Cloning of the genes for degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine from Rhodococcus sp. strain TE1.	Shao ZQ, Behki R.	Appl Environ Microbiol	10.1128/aem.61.5.2061-2065.1995	1995
Enzymology	Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems.	de los Reyes FL, Ritter W, Raskin L.	Appl Environ Microbiol	10.1128/aem.63.3.1107-1117.1997	1997
Phylogeny	Comparison of Actinobacteria communities from human-impacted and pristine karst caves.	Buresova-Faitova A, Kopecky J, Sagova-Mareckova M, Alonso L, Vautrin F, Moenne-Loccoz Y, Rodriguez-Nava V.	Microbiologyopen	10.1002/mbo3.1276	2022
	iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments.	Dos Santos JDN, Joao SA, Martin J, Vicente F, Reyes F, Lage OM.	Microorganisms	10.3390/microorganisms10071471	2022

References

#10971	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43347
#18486	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 )
#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 )
#34042	; 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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#118743	Collection of Institut Pasteur ; Curators of the CIP; CIP 104178
#124042	Johannes Wittmann, Clara Rolland, Lorenz Reimer, Joaquim Sardà: PhageDive .
#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 coprophilus (DSM 43347, ATCC 29080, CUB 687)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Phages

Sequence information

Genome sequences

Genome browser: GCA_900478115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media