Actinomadura macra (DSM 43862, ATCC 31286, IFO 14102)

Name: Actinomadura macra (DSM 43862, ATCC 31286, IFO 14102)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16932

Type strain

Strain Designation FD 25934, A-0287

Culture col. no. DSM 43862 ATCC 31286 IFO 14102 IMET 9754 JCM 3287 16 more

NCBI tax ID(s) 1220564 46164

Special Collections DSMZ JCM KCTC CIP Wink compendium JMRC

History DSMZ <- JCM <- KCC <- Chas. Pfizer & Co., FD 25934 JCM <-- KCC A-0287 <-- Chas. Pfizer & Co.; FD 25934. CIP <- 1998, JCM <- KCC: strain A-0287 <- Chas, Pfizer & Co.: strain FD 25934

Links

Actinomadura macra FD 25934 is an obligate aerobe, Gram-positive, rod-shaped bacterium that builds an aerial mycelium and was isolated from soil.

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

Name and taxonomic classification

SI-ID 39984

MTCC 2559,ATCC 31286,NRRL B-16124,CIP 105532,JCM 3287,DSM 43862,IFO 14102,IMET 9754,CCRC 13378,KCTC 9342,NBRC 14102,BCRC 13378,CGMCC 4.1513

@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 macra

Full scientific name Actinomadura macra (ex Celmer et al. 1979) Huang 1980

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	positive		99.326
125439			95.69
120741	positive	rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
19972	Red brown (8012)	10-14 days	ISP 2
19972	Colorless	10-14 days	ISP 3
19972	Colorless	10-14 days	ISP 4
19972	Beige (1001)	10-14 days	ISP 5
19972	Beige (1001)	10-14 days	ISP 6
19972	Colorless	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19972	Aerial Mycelium	White	ISP 2
19972			ISP 3
19972			ISP 4
19972			ISP 5
19972			ISP 6
19972			ISP 7

Multimedia

@ref:	11344
multimedia content:	DSM_43862.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43862.jpg
caption:	Medium 65 28°C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19972	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
19972	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:
19972	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
19972	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
19972	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
19972	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
34048	MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11344	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
120741	CIP Medium 116	Medium recipe at CIP
120741	CIP Medium 194	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11344	positive	growth	28
19972	positive	optimum	28
34048	positive	growth	30
67770	positive	growth	28
120741	positive	growth	25-37
120741	negative	growth	5
120741	negative	growth	15
120741	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120741	obligate aerobe
125439	facultative anaerobe	96.876

Compound production

@ref	Compound
20216	Antibiotic CP 47433
20216	Antibiotic CP 47434
19972	Polyether antibiotic, active against gram-positive, shows anticoccidial activity
67770	Antibiotics CP-47433 and CP-47434

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19972	NaCl	positive	maximum	2.5 %
120741	NaCl	positive	growth	0 %
120741	NaCl		growth	2 %
120741	NaCl		growth	4 %
120741	NaCl		growth	6 %
120741	NaCl		growth	8 %
120741	NaCl		growth	10 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19972	22599 ChEBI	arabinose	-
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
19972	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
120741	4853 ChEBI	esculin	-	hydrolysis
19972	28757 ChEBI	fructose	-
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19972	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	+	degradation	from API 20E
19972	29864 ChEBI	mannitol	-
19972	17268 ChEBI	myo-inositol	-
120741	17632 ChEBI	nitrate	+	reduction
120741	17632 ChEBI	nitrate	-	respiration
120741	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
19972	16634 ChEBI	raffinose	-
19972	26546 ChEBI	rhamnose	-
19972	17992 ChEBI	sucrose	-
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
19972	18222 ChEBI	xylose	-

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
120741	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
120741	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
120741	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+			from API 20E
120741	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
120741	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	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
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
120741	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
120741	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase lipase (C 8)	+		from API zym
120741	gamma-glutamyltransferase	+	2.3.2.2
120741	gelatinase	-
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
120741	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
120741	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
120741	oxidase	-
120741	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
120741	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
120741	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
19972	-	+	+	+	+	-	+	-	-	+	+	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
19972	not determinedn.d.	-	-	+	+	+	+	-	-	+	-	-	-	-	-	+	-	+	-	-
120741	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11344	soil	Okayama	Japan	JPN	Asia
67770	Soil	Okayama	Japan	JPN	Asia
120741	Environment, Soil	Okayama	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence U49009 (>99% sequence identity) for Actinomadura from Microbeatlas

Aquatic Samples	4
Soil Samples	72
Animal Samples	3
Plant Samples	0
Total Samples	79

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11344	1	Risk group (German classification) According to TRBA 466
19972	1	German classification According to TRBA 466
120741	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	ASM155221v1 assembly for Actinomadura macra NBRC 14102	contig	GCA_001552215	1220564.3	2731957575	1220564	59.03

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomadura macra 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134102	450	46164
20218	Actinomadura macra 16S rRNA gene	U49009	1403	46164
20218	Actinomadura macra gene for 16S rRNA, partial sequence, strain: NBRC 14102	AB364594	1471	46164

GC content

@ref	GC-content (mol%)	Method
67770	70.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM155221v1 assembly for Actinomadura macra NBRC 14102
NCBI: GCA_001552215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.88	no
125439	gram_stain	BacteriaNetⓘ	positive	99.33	no
125439	motility	BacteriaNetⓘ	no	95.69	no
125439	spore_formation	BacteriaNetⓘ	yes	88.13	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura macra NBRC 14102
PATRIC: 1220564.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.86	no
125438	anaerobic	anaerobicⓘ	no	94.68	yes
125438	spore-forming	spore-formingⓘ	yes	86.43	no
125438	aerobic	aerobicⓘ	yes	89.82	yes
125438	thermophilic	thermophileⓘ	no	94.00	yes
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Bacterial catabolism of acetovanillone, a lignin-derived compound.	Dexter GN, Navas LE, Grigg JC, Bajwa H, Levy-Booth DJ, Liu J, Louie NA, Nasseri SA, Jang SK, Renneckar S, Eltis LD, Mohn WW.	Proc Natl Acad Sci U S A	10.1073/pnas.2213450119	2022
	Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction.	Omori WP, Pinheiro DG, Kishi LT, Fernandes CC, Fernandes GC, Gomes-Pepe ES, Pavani CD, Lemos EGM, Souza JAM.	Genet Mol Biol	10.1590/1678-4685-gmb-2017-0376	2019
Phylogeny	Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya.	Cao P, Xu X, Li C, Han L, Mu W, Xiang W, Zhao J, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004708	2021

References

#11344	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43862
#19972	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 )
#34048	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#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 .
#120741	Collection of Institut Pasteur ; Curators of the CIP; CIP 105532
#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 macra (DSM 43862, ATCC 31286, IFO 14102)

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

Compound production

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001552215

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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