Actinomadura meyerae (DSM 44715, NRRL B-24247, A288)

Name: Actinomadura meyerae (DSM 44715, NRRL B-24247, A288)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16989

Type strain

Strain Designation A288

Culture col. no. DSM 44715 NRRL B-24247 A288 JCM 13237 CIP 108410

NCBI tax ID(s) 240840

Special Collections DSMZ JCM Wink compendium CIP

Links

Actinomadura meyerae A288 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from garden soil.

Gram-positive obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 131406

DSM 44715,NRRL B-24247,JCM 13237,CIP 108410

@ref 20215

Last LPSN update 2025-12-16 09:50:58

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinomadura

Species Actinomadura meyerae

Full scientific name Actinomadura meyerae corrig. Quintana et al. 2004

Synonyms (1)

Actinomadura meyerii

Morphology

Cell morphology

@ref	Motility	Confidence
125438		90.5
125439		99.8
120932

Colony morphology

@ref	Colony color	Incubation period	Medium used
19694	Beige	10-14 days	ISP 2
19694	Beige	10-14 days	ISP 3
19694	Beige	10-14 days	ISP 4
19694		10-14 days	ISP 5
19694	Beige	10-14 days	ISP 6
19694	Beige	10-14 days	ISP 7
120932

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19694		ISP 2
19694		ISP 3
19694		ISP 4
19694		ISP 5
19694		ISP 6
19694		ISP 7

Multimedia

@ref:	12034
multimedia content:	DSM_44715.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44715.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12034	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
12034	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
19694	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
19694	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:
19694	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
19694	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
19694	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
19694	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
33963	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum		Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
120932	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12034	positive	growth	28	mesophilic
19694	positive	optimum	28	mesophilic
33963	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
120932	obligate aerobe
125438	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		93.4

Observation

67770

Observationquinones: MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120932	17632 ChEBI	nitrate	+	reduction
120932	17632 ChEBI	nitrate	-	respiration
120932	16301 ChEBI	nitrite	-	reduction

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120932	alcohol dehydrogenase	-	1.1.1.1
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120932	catalase	+	1.11.1.6
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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120932	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120932	ornithine decarboxylase	-	4.1.1.17
120932	oxidase	+
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	3-chlorocatechol degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	dTDPLrhamnose biosynthesis	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	starch degradation	100	10 of 10
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	butanoate fermentation	100	4 of 4
66794	urea cycle	100	13 of 13
66794	methylglyoxal degradation	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	cellulose degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	photosynthesis	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	myo-inositol biosynthesis	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	d-mannose degradation	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	purine metabolism	87.23	82 of 94
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	flavin biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	aclacinomycin biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	tryptophan metabolism	81.58	31 of 38
66794	factor 420 biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	histidine metabolism	79.31	23 of 29
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	toluene degradation	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	cholesterol biosynthesis	72.73	8 of 11
66794	oxidative phosphorylation	72.53	66 of 91
66794	degradation of hexoses	72.22	13 of 18
66794	cysteine metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	sulfate reduction	69.23	9 of 13
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	lysine metabolism	69.05	29 of 42
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	vitamin B12 metabolism	64.71	22 of 34
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	degradation of pentoses	64.29	18 of 28
66794	ascorbate metabolism	63.64	14 of 22
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	carotenoid biosynthesis	59.09	13 of 22
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	chlorophyll metabolism	55.56	10 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	D-cycloserine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	arachidonic acid metabolism	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	methanogenesis from CO2	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4

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
19694	not determinedn.d.	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-
120932	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Garden

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12034	garden soil	Mexico City	Mexico	MEX	North America
67770	Garden soil	Mexico City	Mexico	MEX	North America
120932	Environment, Garden soil		Mexico	MEX	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12034	1	Risk group (German classification) According to TRBA 466
120932	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	IMG-taxon 2700988714 annotated assembly for Actinomadura meyerae DSM 44715	scaffold	GCA_900188445	240840.3	2700988714	240840	50.1

Genome browser: GCA_900188445

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12034	Actinomadura meyerii A288 16S ribosomal RNA gene, partial sequence	AY273787	1480		240840

GC content

@ref	GC-content (mol%)	Method
67770	72.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinomadura meyerae DSM 44715
NCBI: GCA_900188445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	93.40	no
125439	motility	BacteriaNetⓘ	no	89.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura meyerae strain DSM 44715
PATRIC: 240840.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.74	no
125438	anaerobic	anaerobicⓘ	no	94.28	yes
125438	spore-forming	spore-formingⓘ	yes	88.79	no
125438	aerobic	aerobicⓘ	yes	91.55	yes
125438	thermophilic	thermophileⓘ	no	92.77	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinomadura xylanilytica sp. nov., an actinomycete isolated from soil.	Zucchi TD, Kim BY, Bonda ANV, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.042325-0	2012
Phylogeny	Actinomadura geliboluensis sp. nov., isolated from soil.	Sazak A, Camas M, Sproer C, Klenk HP, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.036145-0	2011

References

#12034	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44715
#19694	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 )
#33963	; Curators of the CIP;
#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;
#68382	Automatically annotated from API zym .
#120932	Collection of Institut Pasteur ; Curators of the CIP; CIP 108410
#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 meyerae (DSM 44715, NRRL B-24247, A288)

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

Spore formation

Observation

Metabolite utilization

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900188445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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