Actinomadura nitritigenes (DSM 44137, IFO 15918, JCM 10104)

Name: Actinomadura nitritigenes (DSM 44137, IFO 15918, JCM 10104)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16976

Type strain

Culture col. no. DSM 44137 IFO 15918 JCM 10104 NBRC 15918 NCIMB 13456 2 more

NCBI tax ID(s) 134602

Special Collections DSMZ JCM Wink compendium

History DSMZ <- A. Lipski, L 46 JCM <-- DSM 44137 <-- A. Lipski L46.

Links

Actinomadura nitritigenes DSM 44137 is a bacterium that builds an aerial mycelium and was isolated from experimental biofilters.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 50504

DSM 44137,IFO 15918,JCM 10104,NCIMB 13456,NBRC 15918,BCRC 16816,CCRC 16816

@ref 20215

Last LPSN update 2026-05-29 08:28:54

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinomadura

Species Actinomadura nitritigenes

Full scientific name Actinomadura nitritigenes Lipski and Altendorf 1995

BacDive ID	Other strains from **Actinomadura nitritigenes** (4)	Type strain
16977	A. nitritigenes DSM 44761, CCUG 46403
16978	A. nitritigenes DSM 44762, CCUG 47067
150704	A. nitritigenes CCUG 41997, DSM 44759
151332	A. nitritigenes CCUG 43780, DSM 44760

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.602

Colony morphology

@ref	Colony color	Incubation period	Medium used
20003	Sand yellow (1002)	10-14 days	ISP 2
20003	Pastel yellow (1034)	10-14 days	ISP 3
20003	Sand yellow (1002)	10-14 days	ISP 4
20003	Sand yellow (1002)	10-14 days	ISP 5
20003	Sand yellow (1002)	10-14 days	ISP 6
20003	Sand yellow (1002)	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
20003			ISP 2
20003			ISP 3
20003	Aerial Mycelium	White	ISP 4
20003	Aerial Mycelium	White	ISP 5
20003			ISP 6
20003	Aerial Mycelium	White	ISP 7

Multimedia

@ref:	11517
multimedia content:	DSM_44137.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44137.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
11517	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
11517	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
20003	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
20003	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:
20003	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
20003	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
20003	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
20003	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
11517	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

Culture temp

@ref	Growth	Type	Temperature (°C)
11517	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.535

Halophily

@ref	Salt	Growth	Tested relation	Concentration
20003	NaCl	positive	growth	0 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20003	22599 ChEBI	arabinose	-
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
20003	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
20003	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
20003	17234 ChEBI	glucose	-
68368	25094 ChEBI	lysine	-	degradation	from API 20E
20003	29864 ChEBI	mannitol	+
20003	17268 ChEBI	myo-inositol	+
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
20003	16634 ChEBI	raffinose	+
20003	26546 ChEBI	rhamnose	-
20003	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
20003	18222 ChEBI	xylose	-

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
20003	-	+	-	-	+	-	-	-	-	+	-	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
20003	not determinedn.d.	+	-	+	-	+	+	+	+	-	+	+	-	-	-	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioremediation	#Biofilter

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11517	experimental biofilters	Osnabrück	Germany	DEU	Europe
67770	Biofilter containing tree bark compost as the packing material

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11517	1	Risk group (German classification) According to TRBA 466
20003	1	German classification According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952429v1 assembly for Actinomadura nitritigenes JCM 10104	scaffold	GCA_039524295	134602	4.92

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomadura nitritigenes 16S ribosomal RNA gene, partial sequence	AY035999	1469	134602
20218	Actinomadura nitritigenes partial 16S rRNA gene, strain IMSNU 21254T	AJ293708	1450	134602
20218	Actinomadura nitritigenes gene for 16S rRNA, partial sequence, strain: NBRC 15918	AB364595	1473	134602

GC content

@ref	GC-content (mol%)	Method
67770	74	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3952429v1 assembly for Actinomadura nitritigenes JCM 10104
NCBI: GCA_039524295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.54	no
125439	gram_stain	BacteriaNetⓘ	positive	99.60	no
125439	motility	BacteriaNetⓘ	no	87.02	no
125439	spore_formation	BacteriaNetⓘ	yes	89.81	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic and Functional Characterization of Culturable Endophytic Actinobacteria Associated With Camellia spp. for Growth Promotion in Commercial Tea Cultivars.	Borah A, Thakur D.	Front Microbiol	10.3389/fmicb.2020.00318	2020
Phylogeny	Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand.	Kanchanasin P, Phongsopitanun W, Yuki M, Kudo T, Ohkuma M, Nakashima T, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.005126	2021
Phylogeny	Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn.	Rachniyom H, Matsumoto A, Inahashi Y, Take A, Takahashi Y, Thamchaipenet A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002714	2018
Phylogeny	Actinomadura montaniterrae sp. nov., isolated from mountain soil.	Songsumanus A, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001196	2016

References

#11517	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44137
#20003	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 )
#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 )
#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 .
#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 nitritigenes (DSM 44137, IFO 15918, JCM 10104)

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

Halophily

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_039524295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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