Micromonospora halophytica (DSM 43171, ATCC 27596, JCM 3125)

Name: Micromonospora halophytica (DSM 43171, ATCC 27596, JCM 3125)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7964

Type strain

Culture col. no. DSM 43171 ATCC 27596 JCM 3125 KCC A-0125 NRRL 2998 10 more

NCBI tax ID(s) 47864

Special Collections DSMZ JCM KCTC Wink compendium

History DSMZ <- KCC <- NRRL <- Schering AG JCM <-- KCC A-0125 <-- NRRL 2998 <-- Schering Corp..

Links

Micromonospora halophytica DSM 43171 is a bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 45819

ATCC 27596,NRRL 2998,JCM 3125,DSM 43171,NCMB 2223,CCRC 11658,IFO 14112,NCIMB 2223,CBS 336.76,AS 4.1078,CECT 3293,KCTC 9551,NBRC 14112,BCRC 11658,CGMCC 4.1078,CGMCC 4.1490

@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 halophytica

Full scientific name Micromonospora halophytica Weinstein et al. 1968 (Approved Lists 1980)

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	92.5
125438	90.622	positive
125439	90.901
125439	98.848	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19553	Orange	10-14 days	ISP 2
19553	Orange - Black	10-14 days	ISP 3
19553	Orange	10-14 days	ISP 4
19553	Orange	10-14 days	ISP 5
19553	Orange	10-14 days	ISP 6
19553	Orange	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19553			ISP 2
19553			ISP 3
19553			ISP 4
19553	Aerial Mycelium	White	ISP 5
19553			ISP 6
19553			ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
10839	CZAPEK PEPTONE AGAR (DSMZ Medium 83)	Medium recipe at MediaDive	Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
19553	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
19553	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:
19553	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
19553	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
19553	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
19553	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
10839	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

Culture temp

@ref	Growth	Type	Temperature (°C)
10839	positive	growth	28
19553	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.485

Spore formation

@ref	Spore formation	Confidence
125438		90.207

Compound production

10839

Compoundhalomycin

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19553	NaCl	positive	maximum	2.5 %

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₆), MK-10(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19553	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
19553	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
19553	28757 ChEBI	fructose	+/-
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19553	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
19553	29864 ChEBI	mannitol	-
19553	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
19553	16634 ChEBI	raffinose	+
19553	26546 ChEBI	rhamnose	-
19553	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
19553	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
67770		halomicin
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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68368	gelatinase	+		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

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
19553	-	-	-	-	-	-	-	-	-	-	+	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.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
10839	salt pool	New York, Syracuse	USA	USA	North America
67770	Mud, bottom of a salt pool	Syracuse, NY	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence X92601 (>99% sequence identity) for Micromonospora from Microbeatlas

Aquatic Samples	188
Soil Samples	470
Animal Samples	133
Plant Samples	13
Total Samples	804

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
10839	1	Risk group (German classification) According to TRBA 466
19553	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	IMG-taxon 2622736531 annotated assembly for Micromonospora halophytica DSM 43171	scaffold	GCA_900090245	47864.4	2622736531	47864	61.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Micromonospora halophytica subsp. halophytica 16S-23S ribosomal RNA spacer region	AF004002	382		47864
10839	Micromonospora halophytica 16S rRNA gene (isolate DSM 43171)	X92601	1476		47864

GC content

@ref	GC-content (mol%)	Method
67770	72.5	high performance liquid chromatography (HPLC)
67770	72.94	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2622736531 annotated assembly for Micromonospora halophytica DSM 43171
NCBI: GCA_900090245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.49	no
125439	gram_stain	BacteriaNetⓘ	positive	98.85	no
125439	motility	BacteriaNetⓘ	no	90.90	no
125439	spore_formation	BacteriaNetⓘ	yes	79.75	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora halophytica strain DSM 43171
PATRIC: 47864.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.62	no
125438	anaerobic	anaerobicⓘ	no	95.56	no
125438	spore-forming	spore-formingⓘ	yes	90.21	no
125438	aerobic	aerobicⓘ	yes	84.52	no
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens.	Santhaseelan H, Dinakaran VT, Dahms HU, Ahamed JM, Murugaiah SG, Krishnan M, Hwang JS, Rathinam AJ.	Microorganisms	10.3390/microorganisms10020417	2022
Metabolism	Characteristics of Inorganic Phosphate-Solubilizing Bacteria from the Sediments of a Eutrophic Lake.	Li Y, Zhang J, Zhang J, Xu W, Mou Z.	Int J Environ Res Public Health	10.3390/ijerph16122141	2019
	Halophiles and Their Biomolecules: Recent Advances and Future Applications in Biomedicine.	Corral P, Amoozegar MA, Ventosa A.	Mar Drugs	10.3390/md18010033	2019
Metabolism	Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites.	Magarvey NA, Keller JM, Bernan V, Dworkin M, Sherman DH.	Appl Environ Microbiol	10.1128/aem.70.12.7520-7529.2004	2004
	Characteristics of airborne actinomycete spores.	Reponen TA, Gazenko SV, Grinshpun SA, Willeke K, Cole EC.	Appl Environ Microbiol	10.1128/aem.64.10.3807-3812.1998	1998
	Transfection in Micromonospora spp.	Caso JL, Hardisson C, Suarez JE.	Appl Environ Microbiol	10.1128/aem.53.10.2544-2547.1987	1987
Genetics	Karakum desert: a unique source of cultivable novel and rare actinomycetes with a remarkable biosynthetic potential.	Saygin H, Sahin N, Goodfellow M.	World J Microbiol Biotechnol	10.1007/s11274-025-04399-3	2025
	Design and optimization of a novel method for extraction of genistein.	Pandit NT, Patravale VB.	Indian J Pharm Sci	10.4103/0250-474x.91583	2011
	Characterization of the Micromonospora rosaria pMR2 plasmid and development of a high G+C codon optimized integrase for site-specific integration.	Hosted TJ, Wang T, Horan AC.	Plasmid	10.1016/j.plasmid.2005.05.004	2005
	Identification, In Vitro Testing and Molecular Docking Studies of Microginins' Mechanism of Angiotensin-Converting Enzyme Inhibition.	Paiva FCR, Ferreira GM, Trossini GHG, Pinto E.	Molecules	10.3390/molecules22121884	2017
Phylogeny	Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness.	Kasai H, Tamura T, Harayama S.	Int J Syst Evol Microbiol	10.1099/00207713-50-1-127	2000
Metabolism	[Production of lincomycin by Micromonospora halophytica culture].	Bibikova MV, Singal EM, Ivanitskaia LP, Zhdanovich IuV.	Antibiot Khimioter		1989
	K-13, a novel inhibitor of angiotensin I converting enzyme produced by Micromonospora halophytica subsp. exilisia. I. Fermentation, isolation and biological properties.	Kase H, Kaneko M, Yamada K.	J Antibiot (Tokyo)	10.7164/antibiotics.40.450	1987
	Actinomycetes: A Never-Ending Source of Bioactive Compounds-An Overview on Antibiotics Production.	De Simeis D, Serra S.	Antibiotics (Basel)	10.3390/antibiotics10050483	2021
	K-13, a novel inhibitor of angiotensin I converting enzyme produced by Micromonospora halophytica subsp. exilisia. II. Structure determination.	Yasuzawa T, Shirahata K, Sano H.	J Antibiot (Tokyo)	10.7164/antibiotics.40.455	1987
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
	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	A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov.	Carro L, Veyisoglu A, Cetin D, Igual JM, Klenk HP, Trujillo ME, Sahin N	Syst Appl Microbiol	10.1016/j.syapm.2018.11.003	2018
Phylogeny	Micromonospora sediminis sp. nov., isolated from mangrove sediment.	Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001175	2016
Phylogeny	Two new species of the genus Micromonospora: Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects.	Fang B, Liu C, Guan X, Song J, Zhao J, Liu H, Li C, Ning W, Wang X, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-015-0472-9	2015
Phylogeny	Micromonospora maritima sp. nov., isolated from mangrove soil.	Songsumanus A, Tanasupawat S, Igarashi Y, Kudo T	Int J Syst Evol Microbiol	10.1099/ijs.0.039180-0	2012
Phylogeny	Micromonospora humi sp. nov., isolated from peat swamp forest soil.	Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo T	Int J Syst Evol Microbiol	10.1099/ijs.0.024281-0	2010

References

#10839	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43171
#19553	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 .
#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 )

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Micromonospora halophytica (DSM 43171, ATCC 27596, JCM 3125)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900090245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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