Micromonospora sonchi (DSM 101530, CGMCC 4.7312, NEAU-QY3)

Name: Micromonospora sonchi (DSM 101530, CGMCC 4.7312, NEAU-QY3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132025

Type strain

Strain Designation NEAU-QY3

Culture col. no. DSM 101530 CGMCC 4.7312 NEAU-QY3 JCM 32497

NCBI tax ID(s) 1763543

Special Collections DSMZ JCM Literature strains

History DSMZ <- Chongxi Liu, Northeast Agricultural Univ., Harbin, China; NEAU-QY3 JCM <-- CGMCC 4.7312 <-- C. Liu; Northeast Agric. Univ., China; NEAU-QY3.

Links

Micromonospora sonchi NEAU-QY3 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from leaves of Sonchus oleraceus.

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

Name and taxonomic classification

SI-ID 404944

JCM 32497,DSM 101530

@ref 20215

Last LPSN update 2026-05-29 08:37:45

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora sonchi

Full scientific name Micromonospora sonchi (Ma et al. 2016) Carro and Oren 2022

Synonyms (1)

Verrucosispora sonchi

Morphology

Cell morphology

@ref	Gram stain	Confidence
25066	positive
125439		94.236
125438	positive	91.15
125439	positive	99.537

Colony morphology

@ref	Colony color	Medium used
25066	moderate orange yellow	Oatmeal agar (ISP3)
25066	Strong orange	NA (Nutrient Agar)

Multimedia

@ref:	23816
multimedia content:	DSM_101530.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_101530.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
23816	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
25066	Oatmeal agar (ISP3)
25066	NA (Nutrient Agar)
23816	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)
23816	positive	growth	28
25066	positive	growth	10.0-40.0
25066	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
25066	positive	optimum	7.0-8.0
25066	positive	growth	7.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25066	aerobe
125439	obligate aerobe	99.543

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
25066	non-motile, single smooth, on substrate hyphae	spore
125438				93.754

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25066	NaCl	positive	growth	0.0-1.0 %(w/v)

Murein

@ref	Murein short key	Type
25066	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25066	2179 ChEBI	6-deoxy-d-galactose	+	carbon source
25066	62968 ChEBI	cellulose	+	hydrolysis
25066	16919 ChEBI	creatine	+	nitrogen source
25066	17108 ChEBI	D-arabinose	-	carbon source
25066	15824 ChEBI	D-fructose	+	carbon source
25066	17634 ChEBI	D-glucose	+	carbon source
25066	16899 ChEBI	D-mannitol	-	carbon source
25066	16024 ChEBI	D-mannose	+	carbon source
25066	16988 ChEBI	D-ribose	-	carbon source
25066	17924 ChEBI	D-sorbitol	+	carbon source
25066	65327 ChEBI	D-xylose	+	carbon source
25066	4853 ChEBI	esculin	+	hydrolysis
25066	16813 ChEBI	galactitol	-	carbon source
25066	15428 ChEBI	glycine	-	nitrogen source
25066	16977 ChEBI	L-alanine	-	nitrogen source
25066	16467 ChEBI	L-arginine	-	nitrogen source
25066	17196 ChEBI	L-asparagine	+	nitrogen source
25066	29991 ChEBI	L-aspartate	+	nitrogen source
25066	29985 ChEBI	L-glutamate	+	nitrogen source
25066	18050 ChEBI	L-glutamine	-	nitrogen source
25066	17203 ChEBI	L-proline	-	nitrogen source
25066	62345 ChEBI	L-rhamnose	-	carbon source
25066	17115 ChEBI	L-serine	-	nitrogen source
25066	16857 ChEBI	L-threonine	-	nitrogen source
25066	17895 ChEBI	L-tyrosine	-	nitrogen source
25066	17716 ChEBI	lactose	-	carbon source
25066	17306 ChEBI	maltose	+	carbon source
25066	17268 ChEBI	myo-inositol	-	carbon source
25066	17632 ChEBI	nitrate	-	reduction
25066	16634 ChEBI	raffinose	+	carbon source
25066	28017 ChEBI	starch	+	hydrolysis
25066	17992 ChEBI	sucrose	+	carbon source
25066	53424 ChEBI	tween 20	-	hydrolysis
25066	53423 ChEBI	tween 40	+	hydrolysis
25066	53426 ChEBI	tween 80	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25066	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
25066	catalase	-	1.11.1.6
25066	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture duration	Enrichment culture temperature
23816	leaves of Sonchus oleraceus	Sonchus oleraceus	Heilongjiang province, Fenghuang Mountain in Wuchang (Harbin)	China	CHN	Asia	44.206	128.056 44.206/128.056
25066	leaves of S. oleraceus L.								21 days	28
67770	Leaves of Sonchus oleraceus from Fenghuang Mountain in Wuchang	Sonchus oleraceus	Heilongjiang Province, north China	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23816	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464623v1 assembly for Micromonospora sonchi CGMCC 4.7312	scaffold	GCA_014646235	1763543.3	2989271904	1763543	52.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23816	Micromonospora sonchi strain NEAU-QY3 16S ribosomal RNA gene, partial sequence	KT633950	1509		1763543

GC content

@ref	GC-content (mol%)	Method
23816	71.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1464623v1 assembly for Micromonospora sonchi CGMCC 4.7312
NCBI: GCA_014646235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.54	no
125439	gram_stain	BacteriaNetⓘ	positive	99.54	no
125439	motility	BacteriaNetⓘ	no	94.24	no
125439	spore_formation	BacteriaNetⓘ	yes	88.97	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Verrucosispora sonchi CGMCC 4.7312
NCBI: GCA_014646235.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.15	no
125438	anaerobic	anaerobicⓘ	no	88.78	no
125438	aerobic	aerobicⓘ	yes	86.21	yes
125438	spore-forming	spore-formingⓘ	yes	93.75	yes
125438	thermophilic	thermophileⓘ	no	90.02	no
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
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

References

#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 )
#23816	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101530
#25066	Z. Z. Ma, S.,Cao, T.,Liu, C.,Huang, Y.,Gao, Y.,Yan, K.,Xiang, W.,Wang, X.: Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.). IJSEM 66: 5430 - 5436 2016 ( DOI 10.1099/ijsem.0.001537 , PubMed 27707427 )
#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;
#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 )

Content

About us

Micromonospora sonchi (DSM 101530, CGMCC 4.7312, NEAU-QY3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014646235

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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