Micromonospora sagamiensis (DSM 43912, ATCC 21826, CIP 108950)

Name: Micromonospora sagamiensis (DSM 43912, ATCC 21826, CIP 108950)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7995

Status isotype of 7978

Type strain

Strain Designation MK-65

Culture col. no. DSM 43912 ATCC 21826 CIP 108950 DSM 44886 JCM 3310 6 more

NCBI tax ID(s) 47875

Special Collections DSMZ JCM KCTC CIP Wink compendium

History DSMZ <- JCM <- KCC <- NRRL <- Kyowa Hakko Co., MK-65 JCM <-- KCC A-0310 <-- NRRL 11334 <-- Kyowa Hakko Kogyo Co., Ltd.; MK-65. CIP <- 2005, DSMZ <- JCM <- KCC <- NRRL <- Kyowa Hakko Co.: strain MK-65

Links

Micromonospora sagamiensis MK-65 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

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

Name and taxonomic classification

SI-ID 37745

ATCC 21826,DSM 43912,JCM 3310,NRRL 11334,KCTC 9215,DSM 44886,KACC 20106,CIP 108950,NBRC 101888

@ref 20215

Last LPSN update 2026-05-29 08:26:46

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora sagamiensis

Full scientific name Micromonospora sagamiensis Kroppenstedt et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122348	positive	rod-shaped
125438	positive		91.563
125439			94.056
125439	positive		99.657

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
19615	Coral red	10-14 days	ISP 2
19615	Salmon pink	10-14 days	ISP 3
19615	Antique pink	10-14 days	ISP 4
19615	Tomato red	10-14 days	ISP 5
19615	Antique pink	10-14 days	ISP 7
122348				0

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19615		ISP 2
19615		ISP 3
19615		ISP 4
19615		ISP 5
19615		ISP 6
19615		ISP 7

Multimedia

@ref:	11263
multimedia content:	DSM_43912.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43912.jpg
caption:	Medium 554 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11263	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
11263	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
19615	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
19615	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:
19615	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
19615	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
19615	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
122348	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11263	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
122348	obligate aerobe
125439	obligate aerobe	98.759

Spore formation

@ref	Spore formation	Confidence
125438		92.183

Compound production

@ref	Compound
11263	micronomicin
19615	Antibiotic XK 62-6
19615	Antibiotic K 144g
19615	Antibiotic 477-2h

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19615	22599 ChEBI	arabinose	-
19615	62968 ChEBI	cellulose	+/-
19615	28757 ChEBI	fructose	-
19615	17234 ChEBI	glucose	-
19615	29864 ChEBI	mannitol	-
19615	17268 ChEBI	myo-inositol	-
122348	17632 ChEBI	nitrate	+	reduction
122348	16301 ChEBI	nitrite	-	reduction
19615	16634 ChEBI	raffinose	+/-
19615	26546 ChEBI	rhamnose	-
19615	17992 ChEBI	sucrose	-
19615	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67770	81283 ChEBI	gentamicin C2b
122348	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122348	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-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-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122348	catalase	+	1.11.1.6
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
122348	lysine decarboxylase	-	4.1.1.18
122348	ornithine decarboxylase	-	4.1.1.17
122348	oxidase	+
122348	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
19615	not determinedn.d.	+	-	+	-	+	-	+	-	-	+	-	+	+	-	+	+	+	-	-
122348	-	+	+	+	+	+	-	-	+	-	+	+	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11263	soil
67770	Forest soil	Sagamihara City, Kanagawa Pref.	Japan	JPN	Asia
122348	Environment, Soil

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11263	1	Risk group (German classification) According to TRBA 466
19615	1	Risk group (German classification) According to TRBA 466
122348	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
66792	ASM1468008v1 assembly for Micromonospora sagamiensis JCM 3310	complete	GCA_014680085	47875.5	8112690325	47875	94.85
66792	ASM782999v1 assembly for Micromonospora sagamiensis DSM 43912	contig	GCA_007829995	47875.4	2585427560	47875	73.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11263	Micromonospora sagamiensis 16S rRNA gene, type strain DSM 43912	X92624	1466		47875

GC content

@ref	GC-content (mol%)	Method
67770	72.51	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1468008v1 assembly for Micromonospora sagamiensis JCM 3310
BV-BRC: 47875.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.76	no
125439	gram_stain	BacteriaNetⓘ	positive	99.66	no
125439	motility	BacteriaNetⓘ	no	94.06	no
125439	spore_formation	BacteriaNetⓘ	yes	86.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora sagamiensis JCM 3310
NCBI: GCA_014680085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.56	no
125438	anaerobic	anaerobicⓘ	no	94.29	yes
125438	aerobic	aerobicⓘ	yes	86.56	yes
125438	spore-forming	spore-formingⓘ	yes	92.18	no
125438	thermophilic	thermophileⓘ	no	92.58	no
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics.	Riesco R, Carro L, Roman-Ponce B, Prieto C, Blom J, Klenk HP, Normand P, Trujillo ME.	Front Microbiol	10.3389/fmicb.2018.01360	2018
Metabolism	Production of antibiotic SU-2 complex by a 2-deoxystreptamine idiotroph of Micromonospora sagamiensis.	Kase H, Kitamura S, Nakayama K.	J Antibiot (Tokyo)	10.7164/antibiotics.35.385	1982
Metabolism	Sagamicin and the related aminoglycosides: fermentation and biosynthesis. III. Isolation and characterization of Micromonospora sagamiensis mutants blocked in gentamicin C1 pathway.	Odakura Y, Kase H, Nakayama K.	J Antibiot (Tokyo)	10.7164/antibiotics.36.125	1983
Metabolism	Multiple-dose pharmacokinetics in serum and sputum of sagamicin administered intramuscularly to patients.	Fraschini F, Scaglione F, Scarpazza G, Marchi M, Braga PC.	Chemotherapy	10.1159/000238479	1987
Metabolism	Sagamicin and the related aminoglycosides: fermentation and biosynthesis. I. Biosynthetic studies with the blocked mutants of Micromonospora sagamiensis.	Kase H, Odakura Y, Nakayama K.	J Antibiot (Tokyo)	10.7164/antibiotics.35.1	1982
Pathogenicity	[Safety evaluation of micronomicin VII. Fertility study by intravenous injection in rats].	Hara T, Fujita T, Takahashi H, Deguchi T.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin VIII. Teratogenicity studies in rabbits after intravenous injection].	Hara T, Fujita T, Takahashi H, Deguchi T.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin IX. Perinatal and postnatal study by intravenous injection in rats].	Hara T, Fujita T, Takahashi H, Deguchi T.	Jpn J Antibiot		1983
Pathogenicity	[Safety evaluation of micronomicin. II. Irritation by repeated intravenous injection in dogs].	Hara T, Nishikawa S, Miyazaki H, Ohguro Y.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin. III. Teratogenicity studies in rats].	Hara T, Nishikawa S, Miyazaki H, Ohguro Y.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin VI. Subacute toxicity in rabbits after drip intravenous infusion].	Hara T, Harada S, Ikenaga T, Yamamoto M, Kashitani J, Deguchi T.	Jpn J Antibiot		1983
Enzymology	Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil.	Carro L, Castro JF, Razmilic V, Nouioui I, Pan C, Igual JM, Jaspars M, Goodfellow M, Bull AT, Asenjo JA, Klenk HP.	Sci Rep	10.1038/s41598-019-38789-z	2019
	[Safety evaluation of micronomicin IV. Acute toxicity in rats, rabbits and dogs after drip intravenous infusion].	Hara T, Harada S, Ikenaga T, Deguchi T.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin V. Subacute toxicity in rats after intravenous injection].	Hara T, Harada S, Yamamoto M, Kashitani J, Deguchi T.	Jpn J Antibiot		1983
	[Safety evaluation of micronomicin. I. Subacute and chronic toxicity in dogs].	Hara T, Nishikawa S, Miyazaki H, Ohguro Y.	Jpn J Antibiot		1983
Pathogenicity	[Review [new antibiotics series III]: micronomicin (author's transl)].	Ohkoshi M, Okada K, Kawamura N.	Jpn J Antibiot		1982
Metabolism	Synthesis of carbon-14 and tritium labeled sagamicin.	Deguchi T, Okumura S, Ishii A, Tanaka M.	J Antibiot (Tokyo)	10.7164/antibiotics.30.993	1977
Enzymology	The gentamicin antibiotics. 6. Gentamicin C2b, an aminoglycoside antibiotic produced by Micromonospora purpurea mutant JI-33.	Daniels PJ, Luce C, Nagabhushan TL.	J Antibiot (Tokyo)	10.7164/antibiotics.28.35	1975
Phylogeny	Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.	Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Goker M, Goodfellow M.	Sci Rep	10.1038/s41598-017-17392-0	2018
	Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms.	Kawamoto I, Oka T, Nara T.	J Bacteriol	10.1128/jb.146.2.527-534.1981	1981
Metabolism	Femtosecond laser-based mutagenesis strategy for micronomicin production enhancement of Micromonospora sagamiensis ATCC 21826.	Liu P, Wen J, Chen Y, Jia X	World J Microbiol Biotechnol	10.1007/s11274-013-1261-0	2013
	Taxonomic description of Micromonospora reichwaldensis sp. nov. and its biosynthetic and plant growth-promoting potential.	Nouioui I, Zimmermann A, Gomez Escribano JP, Jando M, Potter G, Neumann-Schaal M, Mast Y.	Microbiol Spectr	10.1128/spectrum.02129-24	2025
Phylogeny	Micromonospora fluostatini sp. nov., isolated from marine sediment.	Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000589	2015
Phylogeny	Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.	Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt E	Syst Appl Microbiol	10.1016/j.syapm.2004.12.011	2005

References

#11263	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43912
#19615	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 )
#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;
#68382	Automatically annotated from API zym .
#122348	Collection of Institut Pasteur ; Curators of the CIP; CIP 108950
#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 )

Content

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Micromonospora sagamiensis (DSM 43912, ATCC 21826, CIP 108950)

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

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014680085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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