Strain identifier

BacDive ID: 132025

Type strain: Yes

Species: Micromonospora sonchi

Strain Designation: NEAU-QY3

Strain history: CGMCC 4.7312 <-- C. Liu; Northeast Agric. Univ., China; NEAU-QY3.

NCBI tax ID(s): 1763543 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 23816

BacDive-ID: 132025

DSM-Number: 101530

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

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

NCBI tax id

  • NCBI tax id: 1763543
  • Matching level: species

strain history

@refhistory
23816<- Chongxi Liu, Northeast Agricultural Univ., Harbin, China; NEAU-QY3
67770CGMCC 4.7312 <-- C. Liu; Northeast Agric. Univ., China; NEAU-QY3.

doi: 10.13145/bacdive132025.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • 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

    • @ref: 20215
    • synonym: Verrucosispora sonchi

@ref: 23816

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micromonosporales

family: Micromonosporaceae

genus: Verrucosispora

species: Verrucosispora sonchi

full scientific name: Verrucosispora sonchi Ma et al. 2016

strain designation: NEAU-QY3

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
25066positiveno
69480positive100

colony morphology

@refcolony colormedium used
25066moderate orange yellowOatmeal agar (ISP3)
25066Strong orangeNA (Nutrient Agar)

multimedia

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23816GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
25066Oatmeal agar (ISP3)yes
25066NA (Nutrient Agar)yes
23816GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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

@refgrowthtypetemperaturerange
25066positivegrowth10.0-40.0
25066positiveoptimum28mesophilic
23816positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25066positivegrowth7.0-9.0alkaliphile
25066positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25066
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
25066non-motile, single smooth, on substrate hyphaesporeyes
69481yes100
69480yes99.588

halophily

  • @ref: 25066
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.0-1.0 %(w/v)

murein

  • @ref: 25066
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2506617108D-arabinose-carbon source
2506616899D-mannitol-carbon source
2506616988D-ribose-carbon source
2506616813galactitol-carbon source
2506615428glycine-nitrogen source
2506617268myo-inositol-carbon source
2506616977L-alanine-nitrogen source
2506616467L-arginine-nitrogen source
2506618050L-glutamine-nitrogen source
2506617203L-proline-nitrogen source
2506662345L-rhamnose-carbon source
2506617115L-serine-nitrogen source
2506616857L-threonine-nitrogen source
2506617895L-tyrosine-nitrogen source
2506617716lactose-carbon source
2506617632nitrate-reduction
2506653424tween 20-hydrolysis
2506653426tween 80-hydrolysis
2506621796-deoxy-d-galactose+carbon source
2506662968cellulose+hydrolysis
2506616919creatine+nitrogen source
2506615824D-fructose+carbon source
2506617634D-glucose+carbon source
2506616024D-mannose+carbon source
2506617924D-sorbitol+carbon source
2506665327D-xylose+carbon source
250664853esculin+hydrolysis
2506617196L-asparagine+nitrogen source
2506629991L-aspartate+nitrogen source
2506629985L-glutamate+nitrogen source
2506617306maltose+carbon source
2506616634raffinose+carbon source
2506628017starch+hydrolysis
2506617992sucrose+carbon source
2506653423tween 40+hydrolysis

metabolite production

  • @ref: 25066
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
25066catalase-1.11.1.6
25066urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture durationenrichment culture temperature
23816leaves of Sonchus oleraceusSonchus oleraceusHeilongjiang province, Fenghuang Mountain in Wuchang (Harbin)ChinaCHNAsia44.206128.056
25066leaves of S. oleraceus L.21 days28
67770Leaves of Sonchus oleraceus from Fenghuang Mountain in WuchangSonchus oleraceusHeilongjiang Province, north ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

  • @ref: 23816
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23816
  • description: Verrucosispora sonchi strain NEAU-QY3 16S ribosomal RNA gene, partial sequence
  • accession: KT633950
  • length: 1509
  • database: ena
  • NCBI tax ID: 1763543

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora sonchi CGMCC 4.7312GCA_014646235scaffoldncbi1763543
66792Verrucosispora sonchi strain CGMCC 4.73121763543.3wgspatric1763543

GC content

  • @ref: 23816
  • GC-content: 71.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.316no
gram-positiveyes92.038yes
anaerobicno99.174yes
aerobicyes91.523no
halophileno94.001yes
spore-formingyes93.213no
thermophileno95.681no
glucose-utilyes86.023yes
motileno93.87no
glucose-fermentno91.331no

External links

@ref: 23816

culture collection no.: DSM 101530, CGMCC 4.7312, JCM 32497

straininfo link

  • @ref: 90398
  • straininfo: 404944

literature

  • topic: Phylogeny
  • Pubmed-ID: 27707427
  • title: Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).
  • authors: Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001537
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sonchus/*microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
23816Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101530Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101530)
25066Z. 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.)10.1099/ijsem.0.001537IJSEM 66: 5430-5436 201627707427
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90398Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404944.1