Actinomadura mexicana (DSM 44485, NRRL B-24203, A290)

Name: Actinomadura mexicana (DSM 44485, NRRL B-24203, A290)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16985

Type strain

Strain Designation A290

Culture col. no. DSM 44485 NRRL B-24203 A290 CIP 108420 JCM 13236

NCBI tax ID(s) 134959

Special Collections DSMZ JCM CIP

History <- M. Goodfellow; A290 (Actinomadura sp.) DSM 44485 <-- M. Goodfellow A290. CIP <- 2004, DSMZ <- M. Goodfellow, UK: strain A290, Actinomadura sp.

Links

Actinomadura mexicana A290 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from garden soil.

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

Name and taxonomic classification

SI-ID 131405

LMG 29179,DSM 44485,NRRL B-24203,JCM 13236,CIP 108420

@ref 20215

Last LPSN update 2026-02-09 11:22:06

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinomadura

Species Actinomadura mexicana

Full scientific name Actinomadura mexicana Quintana et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
125439	positive			99.7
120927	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11811	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11811	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
33240	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120927	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11811	positive	growth	28
33240	positive	growth	30
67770	positive	growth	28
120927	positive	growth	30-41
120927	negative	growth	5
120927	negative	growth	15
120927	negative	growth	22

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120927	obligate aerobe
125438	aerobe	90.948
125439	obligate aerobe	96.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120927	NaCl	positive	growth	0-2 %
120927	NaCl		growth	4 %
120927	NaCl		growth	6 %
120927	NaCl		growth	8 %
120927	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120927	17632 ChEBI	nitrate	-	reduction
120927	17632 ChEBI	nitrate	-	respiration
120927	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120927	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
120927	15688 ChEBI	acetoin	-
120927	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120927	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
120927	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120927	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
120927	gamma-glutamyltransferase	-	2.3.2.2
120927	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120927	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
120927	ornithine decarboxylase	-	4.1.1.17
120927	oxidase	-
120927	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
120927	tryptophan deaminase	-
120927	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	myo-inositol biosynthesis	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	urea cycle	100	13 of 13
66794	glycogen metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	4-hydroxymandelate degradation	100	9 of 9
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	propanol degradation	100	7 of 7
66794	lipoate biosynthesis	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	3-chlorocatechol degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
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	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	purine metabolism	86.17	81 of 94
66794	aclacinomycin biosynthesis	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	tryptophan metabolism	84.21	32 of 38
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	factor 420 biosynthesis	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	pyrimidine metabolism	77.78	35 of 45
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	non-pathway related	76.32	29 of 38
66794	alanine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	cyclohexanol degradation	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	cholesterol biosynthesis	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	tyrosine metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	oxidative phosphorylation	69.23	63 of 91
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	degradation of pentoses	64.29	18 of 28
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	creatinine degradation	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	arachidonic acid metabolism	55.56	10 of 18
66794	ascorbate metabolism	54.55	12 of 22
66794	carotenoid biosynthesis	54.55	12 of 22
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	bacilysin biosynthesis	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	methanogenesis from CO2	25	3 of 12
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
120927	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	+	-	-	-	-

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
11811	garden soil	Mexico City	Mexico	MEX	North America
67770	Garden soil	Mexico City	Mexico	MEX	North America
120927	Environment, Garden soil		Mexico	MEX	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11811	1	Risk group (German classification) According to TRBA 466
120927	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 2724679706 annotated assembly for Actinomadura mexicana DSM 44485	contig	GCA_900188105	134959.3	2724679706	134959	64.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Actinomadura mexicana gene for 16S ribosomal RNA, partial sequence, strain: A290	AB821481	646		134959
20218	Actinomadura mexicana 16S ribosomal RNA gene, partial sequence	AF277195	1421		134959

GC content

@ref	GC-content (mol%)	Method
67770	72.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinomadura mexicana DSM 44485
NCBI: GCA_900188105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	89.20	no
125439	motility	BacteriaNetⓘ	no	88.60	no
125439	gram_stain	BacteriaNetⓘ	positive	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura mexicana strain DSM 44485
PATRIC: 134959.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.74	no
125438	anaerobic	anaerobicⓘ	no	94.76	yes
125438	spore-forming	spore-formingⓘ	yes	89.86	no
125438	aerobic	aerobicⓘ	yes	90.95	yes
125438	thermophilic	thermophileⓘ	no	93.50	yes
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521(T) as Actinomadura lepetitiana sp. nov.	Dalmastri C, Gastaldo L, Berini F, Marinelli F, Marcone GL	Int J Syst Evol Microbiol	10.1099/ijsem.0.004348	2020
Phylogeny	Actinomadura mexicana sp. nov. and Actinomadura meyerii sp. nov., two novel soil sporoactinomycetes.	Quintana ET, Trujillo ME, Goodfellow M	Syst Appl Microbiol	10.1078/072320203770865800	2003

References

#11811	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44485
#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 )
#33240	; 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 .
#120927	Collection of Institut Pasteur ; Curators of the CIP; CIP 108420
#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 mexicana (DSM 44485, NRRL B-24203, A290)

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 zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900188105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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