Micromonospora yangpuensis (DSM 45577, CGMCC 4.5736, NBRC 107727)

Name: Micromonospora yangpuensis (DSM 45577, CGMCC 4.5736, NBRC 107727)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8019

Type strain

Strain Designation FXJ6.011

Culture col. no. DSM 45577 CGMCC 4.5736 NBRC 107727 FXJ6.011 JCM 18319

NCBI tax ID(s) 683228

Special Collections DSMZ JCM Literature strains

History DSMZ <- Y. Huang, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; FXJ6.011 <- Y. Fan JCM <-- CGMCC 4.5736 <-- L. Zhang et al. FXJ6.011.

Links

Micromonospora yangpuensis FXJ6.011 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from cup-shaped sponge.

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

Name and taxonomic classification

SI-ID 399357

NBRC 107727,DSM 45577

@ref 20215

Last LPSN update 2026-05-29 08:26:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora yangpuensis

Full scientific name Micromonospora yangpuensis Zhang et al. 2012

Morphology

Cell morphology

@ref	Confidence	Gram stain
30103		positive
125439	95.432
125439	99.516	positive

Pigmentation

30103

Productionyes

Multimedia

@ref:	17669
multimedia content:	DSM_45577.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45577.jpg
caption:	Medium 553 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17669	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
17669	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
17669	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)
17669	positive	growth	28
30103	positive	growth	10-45
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
30103	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30103	aerobe
125439	obligate aerobe	99.254

Spore formation

@ref	Spore formation	Confidence
30103
125439		97.414

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30103	NaCl	positive	growth	3 %

Observation

67770

Observationquinones: MK-10(H₂), MK-10(H₄), MK-10(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30103	16449 ChEBI	alanine	+	carbon source
30103	4853 ChEBI	esculin	+	hydrolysis
30103	17754 ChEBI	glycerol	+	carbon source
30103	29864 ChEBI	mannitol	+	carbon source
30103	17632 ChEBI	nitrate	+	reduction
30103	26271 ChEBI	proline	+	carbon source
30103	16634 ChEBI	raffinose	+	carbon source
30103	17822 ChEBI	serine	+	carbon source
30103	17992 ChEBI	sucrose	+	carbon source
30103	53424 ChEBI	tween 20	+	carbon source
30103	53425 ChEBI	tween 60	+	carbon source
30103	53426 ChEBI	tween 80	+	carbon source
30103	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30103	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	phenylmercury acetate degradation	100	2 of 2
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	daunorubicin biosynthesis	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	propionate fermentation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	histidine metabolism	79.31	23 of 29
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	lipid metabolism	77.42	24 of 31
66794	urea cycle	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	alanine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	citric acid cycle	71.43	10 of 14
66794	degradation of pentoses	71.43	20 of 28
66794	oxidative phosphorylation	71.43	65 of 91
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	vitamin B1 metabolism	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	carotenoid biosynthesis	68.18	15 of 22
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	tyrosine metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	carnitine metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	arachidonate biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	vitamin B12 metabolism	47.06	16 of 34
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	sulfate reduction	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Porifera (Sponges)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17669	cup-shaped sponge	South China Sea, Dachan reef	China	CHN	Asia
67770	Cup-shaped sponge at Dachan reef in the South China Sea

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17669	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 2623620524 annotated assembly for Micromonospora yangpuensis DSM 45577	contig	GCA_900091615	683228.4	2623620524	683228	74.34
66792	ASM1464577v1 assembly for Micromonospora yangpuensis CGMCC 4.5736	scaffold	GCA_014645775	683228.9	8112836026	683228	66.98

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17669	Micromonospora yangpuensis strain FXJ6.011 16S ribosomal RNA gene, partial sequence	GU002071	1477		683228

GC content

@ref	GC-content (mol%)	Method
17669	71.3	thermal denaturation, midpoint method (Tm)
30103	71.3
67770	72.02	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 2623620524 annotated assembly for Micromonospora yangpuensis DSM 45577
NCBI: GCA_900091615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.25	no
125439	gram_stain	BacteriaNetⓘ	positive	99.52	no
125439	motility	BacteriaNetⓘ	no	95.43	no
125439	spore_formation	BacteriaNetⓘ	yes	97.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora yangpuensis CGMCC 4.5736
NCBI: GCA_014645775.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.92	yes
125438	anaerobic	anaerobicⓘ	no	92.44	yes
125438	aerobic	aerobicⓘ	yes	89.12	yes
125438	spore-forming	spore-formingⓘ	yes	89.09	yes
125438	thermophilic	thermophileⓘ	no	92.50	no
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Bioactive Metabolites from Terrestrial and Marine Actinomycetes.	Ngamcharungchit C, Chaimusik N, Panbangred W, Euanorasetr J, Intra B.	Molecules	10.3390/molecules28155915	2023
	Intramolecular C-C Bond Formation Links Anthraquinone and Enediyne Scaffolds in Tiancimycin Biosynthesis.	Gui C, Kalkreuter E, Liu YC, Adhikari A, Teijaro CN, Yang D, Chang C, Shen B.	J Am Chem Soc	10.1021/jacs.2c08957	2022
	Unveiling the bioactive potential of Actinomycetota from the Tagus River estuary.	Dos Santos JDN, Pinto E, Martin J, Vicente F, Reyes F, Lage OM.	Int Microbiol	10.1007/s10123-024-00483-0	2024
Genetics	Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22.	Chen SJ, Lam MQ, Thevarajoo S, Abd Manan F, Yahya A, Chong CS.	3 Biotech	10.1007/s13205-020-2148-z	2020
Genetics	Challenges and opportunities for natural product discovery, production, and engineering in native producers versus heterologous hosts.	Teijaro CN, Adhikari A, Shen B.	J Ind Microbiol Biotechnol	10.1007/s10295-018-2094-5	2019
	Natural Products from Actinobacteria as a Potential Source of New Therapies Against Colorectal Cancer: A Review.	Bahrami Y, Bouk S, Kakaei E, Taheri M.	Front Pharmacol	10.3389/fphar.2022.929161	2022
Biotechnology	Yield improvement of enediyne yangpumicins in Micromonospora yangpuensis through ribosome engineering and fermentation optimization.	Wang Z, Sun R, Li M, Liu L, Duan Y, Huang Y	Biotechnol J	10.1002/biot.202100250	2021
Pathogenicity	Yangpumicins F and G, Enediyne Congeners from Micromonospora yangpuensis DSM 45577.	Wang Z, Wen Z, Liu L, Zhu X, Shen B, Yan X, Duan Y, Huang Y	J Nat Prod	10.1021/acs.jnatprod.9b00229	2019
Genetics	Genome Mining of Micromonospora yangpuensis DSM 45577 as a Producer of an Anthraquinone-Fused Enediyne.	Yan X, Chen JJ, Adhikari A, Yang D, Crnovcic I, Wang N, Chang CY, Rader C, Shen B	Org Lett	10.1021/acs.orglett.7b03120	2017
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 spongicola sp. nov., an actinomycete isolated from a marine sponge in the Gulf of Thailand.	Supong K, Suriyachadkun C, Pittayakhajonwut P, Suwanborirux K, Thawai C	J Antibiot (Tokyo)	10.1038/ja.2013.35	2013
Phylogeny	Micromonospora yangpuensis sp. nov., isolated from a sponge.	Zhang L, Xi L, Ruan J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.029439-0	2011

References

#17669	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45577
#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 )
#26459	IJSEM 272 2012 ( DOI 10.1099/ijs.0.029439-0 , PubMed 21398502 )
#30103	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 #26459
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 yangpuensis (DSM 45577, CGMCC 4.5736, NBRC 107727)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900091615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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