Actinomadura citrea (DSM 43461, ATCC 27887, IMET 9573)

Name: Actinomadura citrea (DSM 43461, ATCC 27887, IMET 9573)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16925

Type strain

Culture col. no. DSM 43461 ATCC 27887 IMET 9573 INA 1849 VKM Ac-1119 13 more

NCBI tax ID(s) 46158

Special Collections DSMZ JCM KCTC Wink compendium JMRC

History DSMZ <- M. Goodfellow <- G.F. Gauze, INA JCM <-- KCC A-0295 <-- MS 2135 <-- ATCC 27887 <-- INA 1849.

Links

Actinomadura citrea DSM 43461 is a spore-forming bacterium that builds an aerial mycelium and was isolated from soil.

spore-forming genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 265448

MTCC 1828,ATCC 27887,NRRL B-16121,DSM 43461,IMET 9573,JCM 3295,CCRC 13352,IFO 14678,VKM Ac-1119,KCTC 9617,NBRC 14678,BCRC 13352,NBIMCC 1033,CGMCC 4.1514

@ref 20215

Last LPSN update 2026-05-29 08:28:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinomadura

Species Actinomadura citrea

Full scientific name Actinomadura citrea Lavrova et al. 1972 (Approved Lists 1980)

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		92.342
125439		99.037	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19572		10-14 days	ISP 2
19572		10-14 days	ISP 3
19572	Bright yellow	10-14 days	ISP 4
19572	Bright yellow	10-14 days	ISP 5
19572		10-14 days	ISP 6
19572	Bright yellow	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19572	Aerial Mycelium	White	ISP 2
19572	Aerial Mycelium	White	ISP 3
19572	Aerial Mycelium		ISP 4
19572			ISP 5
19572			ISP 6
19572			ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19572	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
19572	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:
19572	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
19572	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
19572	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
19572	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
11036	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
11036	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
11036	positive	growth	28
19572	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.692
125439	obligate aerobe	97.19

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
19572	Formation of spores, spore surface smooth	spore
125438				90.557

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₆), MK-9(H₈), MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
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
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

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
19572	+	+	+	+	+	-	+	-	-	+	+	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
19572	not determinedn.d.	+	+	+	+	+	+	+	-	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
11036	soil
67770	Soil

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19572	1	Risk group (German classification) According to TRBA 466
11036	1	Risk group (German 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	ASM1340904v1 assembly for Actinomadura citrea DSM 43461	contig	GCA_013409045	46158.3	2844992467	46158	74.33
66792	ASM1464845v1 assembly for Actinomadura citrea JCM 3295	scaffold	GCA_014648455	46158.4	8112911839	46158	54.15

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomadura citrea strain ATCC27887 16S ribosomal RNA gene, partial sequence	AF051377	117	46158
20218	Actinomadura citrea 16S rRNA gene, strain DSM 43461T	AJ420139	1447	46158
20218	Actinomadura citrea 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134091	446	46158
20218	Actinomadura citrea 16S rRNA gene	U49001	1410	46158
124043	Actinomadura citrea strain JCM 3295 16S ribosomal RNA gene, partial sequence.	MT760438	1380	46158

GC content

@ref	GC-content (mol%)	Method
11036	67.6
67770	67.6	thermal denaturation, midpoint method (Tm)
67770	68	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1340904v1 assembly for Actinomadura citrea DSM 43461
NCBI: GCA_013409045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.19	no
125439	gram_stain	BacteriaNetⓘ	positive	99.04	no
125439	motility	BacteriaNetⓘ	no	92.34	no
125439	spore_formation	BacteriaNetⓘ	yes	76.64	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura citrea JCM 3295
NCBI: GCA_014648455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.60	no
125438	anaerobic	anaerobicⓘ	no	95.34	no
125438	aerobic	aerobicⓘ	yes	90.69	no
125438	spore-forming	spore-formingⓘ	yes	90.56	yes
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Molecular-genetic and chemotaxonomic studies on Actinomadura and Nocardiopsis.	Fischer A, Kroppenstedt RM, Stackebrandt E.	J Gen Microbiol	10.1099/00221287-129-11-3433	1983
Phylogeny	Numerical taxonomy of Actinomadura and related actinomycetes.	Goodfellow M, Alderson G, Lacey J.	J Gen Microbiol	10.1099/00221287-112-1-95	1979
Metabolism	Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence.	Patrauchan MA, Florizone C, Dosanjh M, Mohn WW, Davies J, Eltis LD.	J Bacteriol	10.1128/jb.187.12.4050-4063.2005	2005
Phylogeny	Actinomadura maheshkhaliensis sp. nov., a novel actinomycete isolated from mangrove rhizosphere soil of Maheshkhali, Bangladesh.	Ara I, Matsumoto A, Abdul Bakir M, Kudo T, Omura S, Takahashi Y.	J Gen Appl Microbiol	10.2323/jgam.54.335	2008

References

#11036	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43461
#19572	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 JMRC: Jena Microbial Resource Collection (JMRC):
#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 )
#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 .
#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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Actinomadura citrea (DSM 43461, ATCC 27887, IMET 9573)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013409045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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