Micromonospora eburnea (DSM 44814, JCM 12345, PCU 238)

Name: Micromonospora eburnea (DSM 44814, JCM 12345, PCU 238)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7982

Type strain

Strain Designation LK2-10

Culture col. no. DSM 44814 JCM 12345 PCU 238 TISTR 1531 LK2-10 3 more

NCBI tax ID(s) 227316

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History DSMZ <- Ch. Thawai; LK2-10 JCM <-- C. Thawai LK2-10. CIP <- 2005, JCM <- 2004, C. Thawai, Chulalongkorn Univ., Bangkok, Thailand: strain LK2-10

Links

Micromonospora eburnea LK2-10 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 135124

DSM 44814,JCM 12345,TISTR 1531,CIP 108667,NBRC 101921,NBRC 101912

@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 eburnea

Full scientific name Micromonospora eburnea Thawai et al. 2005

BacDive ID	Other strains from **Micromonospora eburnea** (1)	Type strain
161218	M. eburnea JCM 12346, PCU 237

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31287	positive
118990	positive	rod-shaped
125439			95.751
125439	positive		99.832
125438	positive		90.715

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
20126	Pastel yellow (1034)	10-14 days	ISP 2
20126	Beige (1001)	10-14 days	ISP 3
20126	Beige (1001)	10-14 days	ISP 4
20126	Beige (1001)	10-14 days	ISP 5
20126	Beige (1001)	10-14 days	ISP 6
20126	Beige (1001)	10-14 days	ISP 7
118990				1

Multicellular morphology

@ref	Complex name	Complex color	Medium name
20126			ISP 2
20126	Aerial Mycelium	White	ISP 3
20126			ISP 4
20126			ISP 5
20126			ISP 6
20126			ISP 7

Pigmentation

31287

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12098	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
12098	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
20126	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
20126	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:
20126	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
20126	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
20126	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
20126	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
36415	MEDIUM 375 - for Catellospora koreensis		Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Agar (15.000 g);Yeast extract (4.000 g);Starch maize (15.000 g);Di Potassium monohydrogenophosphate (0.500 g)
12098	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
12098	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
118990	CIP Medium 375	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12098	positive	growth	28
20126	positive	optimum	28
31287	positive	optimum	27.5
36415	positive	growth	25
67770	positive	growth	28
118990	positive	growth	25-45
118990	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31287	aerobe
118990	obligate aerobe
125439	obligate aerobe	98.743

Spore formation

@ref	Spore formation	Confidence
31287
125439		95.459
125438		93.15

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31287	NaCl	positive	growth	<4 %
118990	NaCl	positive	growth	0-2 %
118990	NaCl		growth	4 %
118990	NaCl		growth	6 %
118990	NaCl		growth	8 %
118990	NaCl		growth	10 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20126	22599 ChEBI	arabinose	+
31287	17057 ChEBI	cellobiose	+	carbon source
20126	62968 ChEBI	cellulose	+/-
118990	16947 ChEBI	citrate	-	carbon source
118990	4853 ChEBI	esculin	+	hydrolysis
20126	28757 ChEBI	fructose	+
31287	28260 ChEBI	galactose	+	carbon source
20126	17234 ChEBI	glucose	+/-
31287	17234 ChEBI	glucose	+	carbon source
31287	17754 ChEBI	glycerol	+	carbon source
118990	606565 ChEBI	hippurate	+	hydrolysis
31287	17716 ChEBI	lactose	+	carbon source
20126	29864 ChEBI	mannitol	+
31287	29864 ChEBI	mannitol	+	carbon source
31287	28053 ChEBI	melibiose	+	carbon source
20126	17268 ChEBI	myo-inositol	+
31287	17632 ChEBI	nitrate	+	reduction
118990	17632 ChEBI	nitrate	+	reduction
118990	17632 ChEBI	nitrate	-	respiration
118990	16301 ChEBI	nitrite	-	reduction
20126	16634 ChEBI	raffinose	+
31287	16634 ChEBI	raffinose	+	carbon source
20126	26546 ChEBI	rhamnose	+/-
31287	26546 ChEBI	rhamnose	+	carbon source
31287	17814 ChEBI	salicin	+	carbon source
20126	17992 ChEBI	sucrose	+/-
20126	18222 ChEBI	xylose	+/-
31287	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118990	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
118990	15688 ChEBI	acetoin	-
118990	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118990	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-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
118990	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
118990	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118990	caseinase	+	3.4.21.50
118990	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118990	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118990	gamma-glutamyltransferase	+	2.3.2.2
31287	gelatinase	+
118990	gelatinase	+
118990	lecithinase	-
118990	lipase	-
118990	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
118990	ornithine decarboxylase	-	4.1.1.17
118990	oxidase	-
118990	phenylalanine ammonia-lyase	-	4.3.1.24
118990	tryptophan deaminase	-
118990	tween esterase	+
118990	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
20126	not determinedn.d.	-	+	+	-	-	-	-	-	-	+	-	+	+	-	+	+	+	+	-
118990	-	-	+	+	+	+	-	-	+	-	+	-	+	+	-	+	+	+	-	-

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
12098	soil	Yala Prefecture	Thailand	THA	Asia
67770	Soil from peat swamp forest	Lankwai, Yala Province	Thailand	THA	Asia
118990	Environment, Soil, forest	Yala	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12098	1	Risk group (German classification) According to TRBA 466
20126	1	German classification According to TRBA 466
118990	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 2622736604 annotated assembly for Micromonospora eburnea DSM 44814	contig	GCA_900090225	227316.5	2622736604	227316	72.56
124043	ASM4268518v1 assembly for Micromonospora eburnea TISTR 1531	scaffold	GCA_042685185			227316	34.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12098	Micromonospora eburnea gene for 16S rRNA, partial sequence, strain:LK2-10	AB107231	1477		227316

GC content

@ref	GC-content (mol%)	Method
12098	71.5
67770	71.5	high performance liquid chromatography (HPLC)
67770	72.12	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 2622736604 annotated assembly for Micromonospora eburnea DSM 44814
NCBI: GCA_900090225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.74	no
125439	gram_stain	BacteriaNetⓘ	positive	99.83	no
125439	motility	BacteriaNetⓘ	no	95.75	no
125439	spore_formation	BacteriaNetⓘ	yes	95.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora eburnea strain DSM 44814
PATRIC: 227316.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.72	yes
125438	anaerobic	anaerobicⓘ	no	94.41	no
125438	spore-forming	spore-formingⓘ	yes	93.15	yes
125438	aerobic	aerobicⓘ	yes	89.13	yes
125438	thermophilic	thermophileⓘ	no	92.35	yes
125438	flagellated	motile2+ⓘ	no	89.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Understanding thioamitide biosynthesis using pathway engineering and untargeted metabolomics.	Eyles TH, Vior NM, Lacret R, Truman AW.	Chem Sci	10.1039/d0sc06835g	2021
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
Phylogeny	Micromonospora yasonensis sp. nov., isolated from a Black Sea sediment.	Veyisoglu A, Carro L, Guven K, Cetin D, Sproer C, Schumann P, Klenk HP, Goodfellow M, Sahin N.	Antonie Van Leeuwenhoek	10.1007/s10482-016-0701-x	2016
Phylogeny	Micromonospora caldifontis sp. nov., isolated from hot spring soil.	Thawai C, Tanasupawat S, Kudo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.003321	2019
Phylogeny	Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).	Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.001537	2016
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	Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger).	Xiang W, Yu C, Liu C, Zhao J, Yang L, Xie B, Li L, Hong K, Wang X	Int J Syst Evol Microbiol	10.1099/ijs.0.055863-0	2013
Phylogeny	Micromonospora equina sp. nov., isolated from soil from a racecourse.	Everest GJ, Meyers PR	Int J Syst Evol Microbiol	10.1099/ijs.0.042929-0	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
Phylogeny	Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest.	Thawai C, Tanasupawat S, Itoh T, Suwanborirux K, Suzuki KI, Kudo T	Int J Syst Evol Microbiol	10.1099/ijs.0.63217-0	2005

References

#12098	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44814
#20126	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 )
#27606	IJSEM 417 2005 ( DOI 10.1099/ijs.0.63217-0 , PubMed 15653911 )
#31287	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27606
#36415	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#118990	Collection of Institut Pasteur ; Curators of the CIP; CIP 108667
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 eburnea (DSM 44814, JCM 12345, PCU 238)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900090225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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