Micromonospora citrea (DSM 43903, ATCC 35571, CIP 108947)

Name: Micromonospora citrea (DSM 43903, ATCC 35571, CIP 108947)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7989

Type strain

Strain Designation 71-97

Culture col. no. DSM 43903 ATCC 35571 CIP 108947 IFO 14025 JCM 3256 8 more

NCBI tax ID(s) 47855

Special Collections DSMZ JCM KCTC CIP Wink compendium

History <- JCM (Micromonospora citrea) <- KCC <- X. Yan, 71-97 KCC A-0256 <-- X. Yan 71-97. CIP <- 2005, DSMZ <- JCM <- KCC <- X. Yan: strain 71-97

Links

Micromonospora citrea 71-97 is a Gram-positive, rod-shaped bacterium that was isolated from lake mud.

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

Name and taxonomic classification

SI-ID 308587

ATCC 35571,NRRL B-16101,IFO 14025,JCM 3256,DSM 43903,CCRC 12535,KCTC 9367,NBRC 14025,BCRC 12535,CIP 108947,CGMCC 4.1269

@ref 20215

Last LPSN update 2026-02-09 11:19:36

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora citrea

Full scientific name Micromonospora citrea Kroppenstedt et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118294	positive	rod-shaped
125438			90.5
125438	positive		90.845
125439	positive		99.3

Colony morphology

@ref	Colony color	Incubation period	Medium used
19613	Pastel orange	10-14 days	ISP 2
19613	Salmon pink	10-14 days	ISP 3
19613	Pastel yellow	10-14 days	ISP 4
19613		10-14 days	ISP 5
19613	Yellow orange	10-14 days	ISP 6
19613		10-14 days	ISP 7
118294

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19613		ISP 2
19613		ISP 3
19613		ISP 4
19613		ISP 5
19613		ISP 6
19613		ISP 7

Multimedia

@ref:	11378
multimedia content:	DSM_43903.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43903.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
11378	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
11378	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
19613	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
19613	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:
19613	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
19613	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
19613	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
19613	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
118294	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11378	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.6

Compound production

19613

CompoundCitreamicin

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19613	22599 ChEBI	arabinose	+
19613	62968 ChEBI	cellulose	+
19613	28757 ChEBI	fructose	-
19613	17234 ChEBI	glucose	+
19613	29864 ChEBI	mannitol	-
19613	17268 ChEBI	myo-inositol	-
118294	17632 ChEBI	nitrate	+	reduction
118294	16301 ChEBI	nitrite	-	reduction
19613	16634 ChEBI	raffinose	-
19613	26546 ChEBI	rhamnose	-
19613	17992 ChEBI	sucrose	+
19613	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118294	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118294	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
118294	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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
118294	lysine decarboxylase	+	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
118294	ornithine decarboxylase	-	4.1.1.17
118294	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
118294	urease	-	3.5.1.5

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
19613	not determinedn.d.	+	+	+	-	+	+	-	+	+	+	+	+	+	-	+	-	+	-	-
118294	-	+	+	+	-	+	-	-	+	+	+	-	-	+	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
11378	lake mud
67770	Lake mud	China	CHN	Asia
118294	Environment, Lake, mud	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11378	1	Risk group (German classification) According to TRBA 466
19613	1	Risk group (German classification) According to TRBA 466
118294	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 2623620569 annotated assembly for Micromonospora citrea DSM 43903	contig	GCA_900090315	47855.4	2623620569	47855	76.51

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11378	Micromonospora citrea 16S rRNA gene, type strain DSM 43903	X92617	1476		47855

GC content

@ref	GC-content (mol%)	Method
67770	73.82	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micromonospora citrea DSM 43903
NCBI: GCA_900090315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	72.70	no
125439	motility	BacteriaNetⓘ	no	82.30	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora citrea strain DSM 43903
PATRIC: 47855.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.85	no
125438	anaerobic	anaerobicⓘ	no	95.11	no
125438	spore-forming	spore-formingⓘ	yes	89.35	no
125438	aerobic	aerobicⓘ	yes	87.28	no
125438	thermophilic	thermophileⓘ	no	93.00	no
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Cytochromes P450 Associated with the Biosyntheses of Ribosomally Synthesized and Post-translationally Modified Peptides.	Zhong G.	ACS Bio Med Chem Au	10.1021/acsbiomedchemau.3c00026	2023
Genetics	Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.	Chouhan U, Gamad U, Choudhari JK.	J Genet Eng Biotechnol	10.1186/s43141-023-00535-4	2023
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
	Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments.	Lin B, Woo S, Philbrick A, Bacsa J, Laskey E, Mehra N, Gondil VS, Mei JA, Jones G, Pavelka MS, Dziejman M, Shutter DA, Melander C, Perritt AM, Jakober R, Shen Y, Chang W-C, Quave CL, Dunman PM, Luedemann G.	mSphere	10.1128/msphere.00367-25	2025
Metabolism	The effect of methylation inhibitors on citreamicin biosynthesis in Micromonospora citrea.	Pearce CJ, Carter GT, Nietsche JA, Borders DB, Greenstein M, Maiese WM.	J Antibiot (Tokyo)	10.7164/antibiotics.44.1247	1991
Metabolism	Citreamicins, novel antibiotics from Micromonospora citrea: isolation, characterization, and structure determination.	Carter GT, Nietsche JA, Williams DR, Borders DB.	J Antibiot (Tokyo)	10.7164/antibiotics.43.504	1990
	Microorganisms Associated with the Marine Sponge Scopalina hapalia: A Reservoir of Bioactive Molecules to Slow Down the Aging Process.	Said Hassane C, Fouillaud M, Le Goff G, Sklirou AD, Boyer JB, Trougakos IP, Jerabek M, Bignon J, de Voogd NJ, Ouazzani J, Gauvin-Bialecki A, Dufosse L.	Microorganisms	10.3390/microorganisms8091262	2020
Pathogenicity	LL-E19085 alpha, a novel antibiotic from Micromonospora citrea: taxonomy, fermentation and biological activity.	Maiese WM, Lechevalier MP, Lechevalier HA, Korshalla J, Goodman J, Wildey MJ, Kuck N, Greenstein M.	J Antibiot (Tokyo)	10.7164/antibiotics.42.846	1989
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
Enzymology	Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients.	Heuer H, Krsek M, Baker P, Smalla K, Wellington EM.	Appl Environ Microbiol	10.1128/aem.63.8.3233-3241.1997	1997
	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 fluminis sp. nov., isolated from mountain river sediment.	Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PA	Int J Syst Evol Microbiol	10.1099/ijsem.0.004554	2020
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

#11378	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43903
#19613	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;
#68382	Automatically annotated from API zym .
#118294	Collection of Institut Pasteur ; Curators of the CIP; CIP 108947
#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 citrea (DSM 43903, ATCC 35571, CIP 108947)

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

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_900090315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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