Name: Actinomadura macra FD 25934
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16932

Type strain:

Species: Actinomadura macra

Strain Designation: FD 25934, A-0287

Culture col. no.: DSM 43862, ATCC 31286, IFO 14102, IMET 9754, JCM 3287, KCC A-0287, NBRC 14102, BCC 49509, BCRC 13378, CGMCC 4.1513, CIP 105532, IMSNU 22164, KCTC 9342, MTCC 2559, NCIMB 14303, NRRL B-16124, TBRC 2223

Strain history: CIP <- 1998, JCM <- KCC: strain A-0287 <- Chas, Pfizer & Co.: strain FD 25934

NCBI tax ID(s): 1220564 (strain), 46164 (species)

SI-ID 39984

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

Special Collections

Other strains from Actinomadura macra

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Streptosporangiales*
	Family	*Thermomonosporaceae*
	Genus	*Actinomadura*
	Species	**Actinomadura macra**
	Full Scientific Name (LPSN)	Actinomadura macra (ex Celmer et al. 1979) Huang 1980

Information on morphological and physiological properties Morphology

[Ref.: #120741]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %99.8

[Ref.: #120741]	Cell shape	rod-shaped

[Ref.: #120741]	Motility	no
[Ref.: #125439]	Motility	no Confidence in %93.4

[Ref.: #19972]	Colony color	Red brown (8012)
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 2

[Ref.: #19972]	Colony color	Colorless
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 3

[Ref.: #19972]	Colony color	Colorless
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 4

[Ref.: #19972]	Colony color	Beige (1001)
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 5

[Ref.: #19972]	Colony color	Beige (1001)
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 6

[Ref.: #19972]	Colony color	Colorless
[Ref.: #19972]	Incubation period	10-14 days
[Ref.: #19972]	Cultivation medium used	ISP 7

[Ref.: #19972]	Multicellular complex forming ability	yes
[Ref.: #19972]	Multicellular complex name	Aerial Mycelium
[Ref.: #19972]	Multicellular complex color	White
[Ref.: #19972]	Medium Name (multicellularity)	ISP 2

[Ref.: #19972]	Multicellular complex forming ability	no
[Ref.: #19972]	Medium Name (multicellularity)	ISP 3

[Ref.: #19972]	Multicellular complex forming ability	no
[Ref.: #19972]	Medium Name (multicellularity)	ISP 4

[Ref.: #19972]	Multicellular complex forming ability	no
[Ref.: #19972]	Medium Name (multicellularity)	ISP 5

[Ref.: #19972]	Multicellular complex forming ability	no
[Ref.: #19972]	Medium Name (multicellularity)	ISP 6

[Ref.: #19972]	Multicellular complex forming ability	no
[Ref.: #19972]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19972]

Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

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Culture medium

MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #120741]

Culture medium

CIP Medium 116

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

CIP Medium 194

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #11344]		growth	28 °C
[Ref.: #19972]		optimum	28 °C
[Ref.: #34048]		growth	30 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #120741]		growth	25-37 °C
[Ref.: #120741]	negative	growth	5 °C
[Ref.: #120741]	negative	growth	15 °C
[Ref.: #120741]	negative	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120741]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.8

[Ref.: #125439]

Ability of spore formation

yes Confidence in %90.5

[Ref.: #20216]	Name of produced compound	Antibiotic CP 47433
[Ref.: #20216]	Name of produced compound	Antibiotic CP 47434
[Ref.: #19972]	Name of produced compound	Polyether antibiotic, active against gram-positive, shows anticoccidial activity
[Ref.: #67770]	Name of produced compound	Antibiotics CP-47433 and CP-47434

	Salt	Tested relation		Salt conc.
[Ref.: #19972]	NaCl		maximum	2.5	%
[Ref.: #120741]	NaCl		growth	0	%
[Ref.: #120741]	NaCl	no	growth	2	%
[Ref.: #120741]	NaCl	no	growth	4	%
[Ref.: #120741]	NaCl	no	growth	6	%
[Ref.: #120741]	NaCl	no	growth	8	%
[Ref.: #120741]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-9(H₆), MK-9(H₈)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19972]	arabinose ChEBI	-
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19972]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #120741]	esculin ChEBI	-	hydrolysis
[Ref.: #19972]	fructose ChEBI	-
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19972]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #19972]	mannitol ChEBI	-
[Ref.: #19972]	myo-inositol ChEBI	-
[Ref.: #120741]	nitrate ChEBI	+	reduction
[Ref.: #120741]	nitrate ChEBI	-	respiration
[Ref.: #120741]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #19972]	raffinose ChEBI	-
[Ref.: #19972]	rhamnose ChEBI	-
[Ref.: #19972]	sucrose ChEBI	-
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19972]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120741]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite	Production
[Ref.: #120741]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #120741]	acetoin ChEBI	-
[Ref.: #120741]	glucose ChEBI		-
[Ref.: #68368]	acetoin ChEBI	+			* from API 20E
[Ref.: #68368]	indole ChEBI			-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #120741]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #120741]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120741]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120741]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #120741]	gelatinase	-
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120741]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #120741]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #120741]	oxidase	-
[Ref.: #120741]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120741]	tryptophan deaminase	-
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #120741]	urease	-	3.5.1.5
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19972]	575	-	+	+	+	+	-	+	-	-	+	+	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:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19972]	765	not determinedn.d.	-	-	+	+	+	+	-	-	+	-	-	-	-	-	+	-	+	-	-
[Ref.: #120741]	8774	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #11344]	Sample type/isolated from	soil
[Ref.: #11344]	Geographic location (country and/or sea, region)	Okayama
[Ref.: #11344]	Country	Japan
[Ref.: #11344]	Country ISO 3 Code	JPN
[Ref.: #11344]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Okayama
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #120741]	Sample type/isolated from	Environment, Soil
[Ref.: #120741]	Geographic location (country and/or sea, region)	Okayama
[Ref.: #120741]	Country	Japan
[Ref.: #120741]	Country ISO 3 Code	JPN
[Ref.: #120741]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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
Total Samples	79

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #19972]	Biosafety level	1	German classification
[Ref.: #11344]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120741]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Actinomadura macra 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134102	450	GenBank ENA	46164 tax ID	*
[Ref.: #20218]	Actinomadura macra 16S rRNA gene	U49009	1403	GenBank ENA	46164 tax ID	*
[Ref.: #20218]	Actinomadura macra gene for 16S rRNA, partial sequence, strain: NBRC 14102	AB364594	1471	GenBank ENA	46164 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Actinomadura macra NBRC 14102	GCA_001552215	contig	GenBank ENA	1220564 tax ID
[Ref.: #66792]	Actinomadura macra NBRC 14102	1220564.3	wgs	PATRIC	1220564 tax ID	*
[Ref.: #66792]	Actinomadura macra NBRC 14102	2731957575	draft	JGI IMG/M	1220564 tax ID	*

[Ref.: #67770]

GC-content

70.7 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura macra NBRC 14102 PATRIC: 1220564.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	87.858	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.683	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	86.43	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.819	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	87.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinomadura macra NBRC 14102 NCBI: GCA_001552215
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	90.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	93.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.8

Availability in culture collections External links

[Ref.: #11344]

Culture collection no.

DSM 43862, ATCC 31286, IFO 14102, IMET 9754, JCM 3287, KCC A-0287, NBRC 14102, BCC 49509, BCRC 13378, CGMCC 4.1513, CIP 105532, IMSNU 22164, KCTC 9342, MTCC 2559, NCIMB 14303, NRRL B-16124, TBRC 2223

[Ref.: #85937]

SI-ID 39984

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) .

#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;

#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 .

#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 .

#85937

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID39984.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Actinomadura macra NBRC 14102

Actinomadura macra NBRC 14102

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