Micromonospora phaseoli (DSM 45730, CGMCC 4.7038, KCTC 39763)

Name: Micromonospora phaseoli (DSM 45730, CGMCC 4.7038, KCTC 39763)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23126

Type strain

Strain Designation NEAU-J5

Culture col. no. DSM 45730 CGMCC 4.7038 KCTC 39763 NBRC 110907 NEAU-J5 1 more

NCBI tax ID(s) 1144548

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

History <- C. Liu, School of Life Science, Northeast Agricultural University, China; NEAU-J5 <- F. Jia CGMCC 4.7038 <-- X. Wang et al.; Northeast Agric. Univ., China; NEAU-J5.

Links

Micromonospora phaseoli NEAU-J5 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from root of snap bean .

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

Name and taxonomic classification

SI-ID 407455

NBRC 110907,DSM 45730

@ref 20215

Last LPSN update 2026-02-09 11:23:40

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora phaseoli

Full scientific name Micromonospora phaseoli (Wang et al. 2013) Nouioui et al. 2018

Synonyms (1)

Xiangella phaseoli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Confidence
30842	positive	0.69 µm	0.6 µm
125438				90
125438	positive			92.875
125439	positive			99.5

Colony morphology

@ref	Colony color	Medium used
69425	Deep orange (2011)	ISP 3
69425	Melon yellow (1028)	ISP 5
69425	Pastel yellow (1034), clay brown (8003)	ISP 4
69425	Pastel yellow (1034), yellow orange (2000), clay brown (8003)	ISP 7
69425	Pastel yellow (134), yellow orange (2000)	suter without tyrosine
69425	Pastel yellow (134), yellow orange (2000), clay brown (8003)	suter with tyrosine
69425	Yellow orange (2000)	ISP 6
69425	Yellow orange (2000), orange brown (8033)	ISP 2

Multicellular morphology

@ref	Complex name	Medium name
69425	Aerial mycelium	ISP 2
69425	Aerial mycelium	ISP 3
69425	Aerial mycelium	ISP 4
69425	Aerial mycelium	ISP 5
69425	Aerial mycelium	ISP 6
69425	Aerial mycelium	ISP 7
69425	Aerial mycelium	suter with tyrosine
69425	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Name
30842
69425		melanin pigment
69425		soluble pigment

Multimedia

@ref:	19333
multimedia content:	DSM_45730.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45730.jpg
caption:	Medium 554 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	69425
multimedia content:	DSM_45730_image3.jpeg
multimedia.multimedia content:	DSM_45730_image3.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69425
multimedia content:	DSM_45730_image4.jpeg
multimedia.multimedia content:	DSM_45730_image4.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19333	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
19333	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
19333	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
19333	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

Culture temp

@ref	Growth	Type	Temperature (°C)
19333	positive	growth	28
30842	positive	growth	18-37
30842	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
30842	positive	optimum	7
30842	positive	growth	05-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30842	aerobe
125439	obligate aerobe	99.5

Spore formation

@ref	Spore formation	Confidence
30842
125438		92.793

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30842	NaCl	positive	growth	0-3 %
69425	NaCl	positive	growth	0-2.5 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69425	22599 ChEBI	arabinose	+	growth
30842	22599 ChEBI	arabinose	+	carbon source
69425	62968 ChEBI	cellulose	+/-	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69425	28757 ChEBI	fructose	+	growth
30842	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
30842	17234 ChEBI	glucose	+	carbon source
69425	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69425	17268 ChEBI	inositol	+/-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
30842	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
30842	29864 ChEBI	mannitol	+	carbon source
30842	37684 ChEBI	mannose	+	carbon source
69425	37684 ChEBI	mannose	+/-	growth
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
30842	16634 ChEBI	raffinose	+	carbon source
69425	16634 ChEBI	raffinose	+/-	growth
30842	26546 ChEBI	rhamnose	+	carbon source
69425	26546 ChEBI	rhamnose	+/-	growth
30842	30911 ChEBI	sorbitol	+	carbon source
30842	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69425	17992 ChEBI	sucrose	+	growth
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69425	18222 ChEBI	xylose	+	growth

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
30842	gelatinase	+
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69425	-	-	-	+	-	-	+	-	-	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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
69425	not determinedn.d.	+	+	+	+/-	+	+/-	+/-	+/-	+	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
19333	root of snap bean (Phaseolus vulgaris L.)	Phaseolus vulgaris	Heilongjiang province, Harbin, (45° 45' N 126° 41' E)	China	CHN	Asia	45.75	126.683 45.75/126.683
67770	Snap bean root from Harbin		Heilongjiang Province, north China	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19333	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	ASM325347v1 assembly for Micromonospora phaseoli DSM 45730	scaffold	GCA_003253475	1144548.5	2728369481	1144548	71.84
67770	IMG-taxon 2675903138 annotated assembly for Micromonospora phaseoli CGMCC 4.7038	scaffold	GCA_900109115	1144548.3	2675903138	1144548	70.81
66792	ASM1686367v1 assembly for Micromonospora phaseoli NBRC 110907	contig	GCA_016863675	1144548.8	8117738045	1144548	55.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19333	Xiangella phaseoli strain NEAU-J5 16S ribosomal RNA gene, partial sequence	JQ073732	1512		1144548

GC content

@ref	GC-content (mol%)	Method
19333	72.2	thermal denaturation, midpoint method (Tm)
30842	72.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micromonospora phaseoli CGMCC 4.7038
NCBI: GCA_900109115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	positive	99.50	no
125439	motility	BacteriaNetⓘ	no	81.90	no
125439	spore_formation	BacteriaNetⓘ	yes	77.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora phaseoli strain NBRC 110907
PATRIC: 1144548.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.88	yes
125438	anaerobic	anaerobicⓘ	no	95.84	yes
125438	spore-forming	spore-formingⓘ	yes	92.79	yes
125438	aerobic	aerobicⓘ	yes	88.23	no
125438	thermophilic	thermophileⓘ	no	94.00	yes
125438	flagellated	motile2+ⓘ	no	90.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
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 tarapacensis sp. nov., a bacterium isolated from a hypersaline lake.	Villalobos AS, Wiese J, Borchert E, Rahn T, Slaby BM, Steiner LX, Kunzel S, Dorador C, Imhoff JF	Int J Syst Evol Microbiol	10.1099/ijsem.0.005109	2021
Phylogeny	Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae.	Wang X, Jia F, Liu C, Zhao J, Wang L, Shen Y, Wang J, Zhang J, Li C, Xiang W	Int J Syst Evol Microbiol	10.1099/ijs.0.045732-0	2012

References

#19333	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45730
#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 )
#27172	IJSEM 2138 2013 ( DOI 10.1099/ijs.0.045732-0 , PubMed 23104362 )
#30842	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 #27172
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69425	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )

Rate our new design

Content

About us

Micromonospora phaseoli (DSM 45730, CGMCC 4.7038, KCTC 39763)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular 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

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003253475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media