Actinomadura rifamycini (DSM 43936, ATCC 33264, IFO 14183)

Name: Actinomadura rifamycini (DSM 43936, ATCC 33264, IFO 14183)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16969

Type strain

Culture col. no. DSM 43936 ATCC 33264 IFO 14183 JCM 3309 KCTC 9248 8 more

NCBI tax ID(s) 1120937 31962

Special Collections DSMZ JCM KCTC Wink compendium

History <- ATCC <- G. F. Gauze, INA KCC A-0309 <-- IFO 14183 <-- ATCC 33264 <-- INA 1349.

Links

Actinomadura rifamycini DSM 43936 is a mesophilic prokaryote that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 40348

PCM 2339,MTCC 3035,ATCC 33264,DSM 43936,IFO 14183,NRRL B-16122,JCM 3309,NCIB 12768,NCIMB 12768,VKM Ac-1085,KCTC 9248,NBRC 14183

@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 rifamycini

Full scientific name Actinomadura rifamycini (Gauze et al. 1987) Promnuan et al. 2011

Synonyms (1)

Actinomadura cremea subsp. rifamycini

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.9

Colony morphology

@ref	Colony color	Incubation period	Medium used
19840	Brown beige	10-14 days	ISP 2
19840	Beige	10-14 days	ISP 3
19840	Beige	10-14 days	ISP 4
19840	Beige	10-14 days	ISP 5
19840	Brown beige	10-14 days	ISP 6
19840	Brown beige	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19840	Aerial Mycelium		ISP 2
19840	Aerial Mycelium	White	ISP 3
19840	Aerial Mycelium	White	ISP 4
19840	Aerial Mycelium	White	ISP 5
19840	Aerial Mycelium	White	ISP 6
19840	Aerial Mycelium	White	ISP 7

Multimedia

@ref:	11386
multimedia content:	DSM_43936.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43936.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
11386	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
19840	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
19840	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:
19840	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
19840	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
19840	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
19840	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
11386	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11386	positive	growth	28	mesophilic
19840	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.202
125439	obligate aerobe	98.8

Spore formation

@ref	Spore formation	Confidence
125439		95.6

Compound production

@ref	Compound
11386	rifamycin
19840	Rifamycin O

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19840	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
19840	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
19840	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19840	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
19840	29864 ChEBI	mannitol	+
19840	17268 ChEBI	myo-inositol	+
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
19840	16634 ChEBI	raffinose	+
19840	26546 ChEBI	rhamnose	+
19840	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
19840	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
67770	26580 ChEBI	rifamycin

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
19840	-	-	-	-	+	-	-	-	-	-	+	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
19840	not determinedn.d.	+	-	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

11386

Sample typesoil

Taxonmaps

69479

Global distribution of 16S sequence U49003 (>99% sequence identity) for Actinomadura rifamycini from Microbeatlas

Aquatic Samples	5
Soil Samples	5
Animal Samples	1
Plant Samples
Total Samples	11

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11386	1	Risk group (German classification) According to TRBA 466
19840	1	Risk group (German 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	ASM42506v1 assembly for Actinomadura rifamycini DSM 43936	scaffold	GCA_000425065	1120937.3	2523533532	1120937	62.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11386	Actinomadura rifamycini gene for 16S rRNA, partial sequence	AB557595	1486		1120937
67770	Actinomadura rifamycini strain IFO 14183 16S ribosomal RNA gene, partial sequence	U49003	1410		1120937

GC content

@ref	GC-content (mol%)	Method
11386	74.5	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: Actinomadura rifamycini DSM 43936
NCBI: GCA_000425065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.60	no
125439	motility	BacteriaNetⓘ	no	87.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura rifamycini DSM 43936
PATRIC: 1120937.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.95	no
125438	anaerobic	anaerobicⓘ	no	93.54	no
125438	spore-forming	spore-formingⓘ	yes	88.80	no
125438	aerobic	aerobicⓘ	yes	90.20	no
125438	thermophilic	thermophileⓘ	no	94.25	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Investigation of Vitamin D₂ and Vitamin D₃ Hydroxylation by Kutzneria albida.	Schmitz LM, Kinner A, Althoff K, Rosenthal K, Lutz S.	Chembiochem	10.1002/cbic.202100027	2021
	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
Genetics	Genome Mining Reveals Rifamycin Biosynthesis in a Taklamakan Desert Actinomycete.	Luo X, Liu Z, Luo X, Xia Z, Wan C, Wang H, Zhang L.	Microorganisms	10.3390/microorganisms13051068	2025
	Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health.	Kim H, Park YH, Yang JE, Kim HS, Kim SC, Oh EJ, Moon J, Cho W, Shin W, Yu C.	Toxics	10.3390/toxics10030117	2022
	Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential.	Jose PA, Jha B.	Sci Rep	10.1038/s41598-017-09672-6	2017
	A calcium-stimulated serine peptidase from a true-branching cyanobacterium, Westiellopsis ramosa sp. nov.	Dubey N, Singh P, Bagchi SN.	Physiol Mol Biol Plants	10.1007/s12298-017-0497-9	2018
Phylogeny	Actinomadura deserti sp. nov., isolated from desert soil.	Cao C, Xu T, Liu J, Cai X, Sun Y, Qin S, Jiang J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002922	2018
Phylogeny	Actinomadura sediminis sp. nov., a marine actinomycete isolated from mangrove sediment.	He J, Xu Y, Sahu MK, Tian XP, Nie GX, Xie Q, Zhang S, Sivakumar K, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.032979-0	2011
Phylogeny	Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov.	Promnuan Y, Kudo T, Ohkuma M, Chantawannakul P	Int J Syst Evol Microbiol	10.1099/ijs.0.026633-0	2010

References

#11386	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43936
#19840	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 )
#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 .
#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 )

Rate our new design

Content

About us

Actinomadura rifamycini (DSM 43936, ATCC 33264, IFO 14183)

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

Compound production

Metabolite utilization

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_000425065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media