Micromonospora pallida (DSM 43817, ATCC 15838, CBS 617.66)

Name: Micromonospora pallida (DSM 43817, ATCC 15838, CBS 617.66)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7973

Type strain

Culture col. no. DSM 43817 ATCC 15838 CBS 617.66 IFO 14110 JCM 3133 11 more

NCBI tax ID(s) 145854

Special Collections DSMZ JCM KCTC Wink compendium

History <- NRRL KCC A-0133 <-- Y. Okami <-- ATCC 15838 <-- Schering Corp. <-- A. Woyciesjes.

Links

Micromonospora pallida DSM 43817 is a bacterium that produces antibiotic compounds and was isolated from soil.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92834

MTCC 708,ATCC 15838,NRRL 2996,JCM 3133,DSM 43817,IFO 14110,IFO 16070,NCIMB 12660,CBS 617.66,CBS 647.71,KCTC 1051,NBRC 14110,NBRC 16070

@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 pallida

Full scientific name Micromonospora pallida (Luedemann and Brodsky 1964) Kasai et al. 2000

Synonyms (1)

Micromonospora echinospora subsp. pallida

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	90.625
125439	positive	99.9
125439		91.8

Colony morphology

@ref	Colony color	Incubation period	Medium used
19596	Saffron yellow	10-14 days	ISP 2
19596	Beige	10-14 days	ISP 3
19596	Saffron yellow	10-14 days	ISP 4
19596		10-14 days	ISP 5
19596		10-14 days	ISP 6
19596	Ochre brown	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19596		ISP 2
19596		ISP 3
19596		ISP 4
19596		ISP 5
19596		ISP 6
19596		ISP 7

Multimedia

@ref:	11290
multimedia content:	DSM_43817.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43817.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
11290	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
19596	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
19596	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:
19596	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
19596	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
19596	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
19596	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
11290	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

Culture temp

@ref	Growth	Type	Temperature (°C)
11290	positive	growth	28
19596	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.094
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125438		92.624

Compound production

11290

Compoundgentamycin

Observation

67770

Observationquinones: MK-12(H₆), MK-12(H₄), MK-12(H₈), MK-11(H₆)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67770	17833 ChEBI	gentamicin

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
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
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
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	+	3.4.21.4	from API zym
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
19596	not determinedn.d.	+	+	+	-	+	-	-	+	-	+	+	-	-	-	+	+	+	-	-

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
11290	soil
67770	Soil	Jamesville, NY	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11290	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 2636415968 annotated assembly for Micromonospora pallida DSM 43817	contig	GCA_900090325	145854.5	2636415968	145854	71.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Micromonospora echinospora subsp. pallida 16S-23S ribosomal RNA spacer region	AF004006	386		145854
11290	M.echinospora 16S rRNA gene (isolate DSM 43817)	X92608	1471		1877

GC content

@ref	GC-content (mol%)	Method
67770	71.1	high performance liquid chromatography (HPLC)
67770	71.88	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micromonospora pallida DSM 43817
NCBI: GCA_900090325

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	89.90	no
125439	motility	BacteriaNetⓘ	no	91.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora pallida strain DSM 43817
PATRIC: 145854.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.63	no
125438	anaerobic	anaerobicⓘ	no	92.71	no
125438	spore-forming	spore-formingⓘ	yes	92.62	no
125438	aerobic	aerobicⓘ	yes	91.09	no
125438	thermophilic	thermophileⓘ	no	91.50	no
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential.	Jose PA, Jha B.	Sci Rep	10.1038/s41598-017-09672-6	2017
	Heterologous expression of the thiopeptide antibiotic GE2270 from Planobispora rosea ATCC 53733 in Streptomyces coelicolor requires deletion of ribosomal genes from the expression construct.	Flinspach K, Kapitzke C, Tocchetti A, Sosio M, Apel AK.	PLoS One	10.1371/journal.pone.0090499	2014
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
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
	Micromonospora cathayae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla.	Long PL, Fu L, Xiao Y, Gao J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006332	2024
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

References

#11290	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43817
#19596	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;
#68382	Automatically annotated from API zym .
#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 pallida (DSM 43817, ATCC 15838, CBS 617.66)

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 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_900090325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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