Strain identifier

BacDive ID: 133064

Type strain: Yes

Species: Micromonospora parathelypteridis

Strain Designation: NEAU-JXY5

Strain history: CGMCC 4.7347 <-- C. Liu; Northeast Agric. Univ., China; NEAU-JXY5.

NCBI tax ID(s): 1839617 (species)

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General

@ref: 24852

BacDive-ID: 133064

DSM-Number: 103125

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

description: Micromonospora parathelypteridis NEAU-JXY5 is an aerobe, spore-forming, Gram-positive bacterium that builds substrate hyphae and was isolated from root of Parathelypteris beddomei Ching.

NCBI tax id

  • NCBI tax id: 1839617
  • Matching level: species

strain history

@refhistory
24852<- C. Liu, School of Life Science, Northeast Agricultural University; NEAU-JXY5 <- S. Zhao
67770CGMCC 4.7347 <-- C. Liu; Northeast Agric. Univ., China; NEAU-JXY5.

doi: 10.13145/bacdive133064.20230509.8.1

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 parathelypteridis
  • full scientific name: Micromonospora parathelypteridis Zhao et al. 2017

@ref: 24852

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora parathelypteridis

full scientific name: Micromonospora parathelypteridis Zhao et al. 2017

strain designation: NEAU-JXY5

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
25195positive
69480positive100

colony morphology

@refcolony colormedium used
25195vivid yellowBennett’s agar
25195brilliant orange yellowISP 2 agar
25195brilliant greenish-yellowISP 3

multicellular morphology

  • @ref: 25195
  • forms multicellular complex: yes
  • complex name: substrate hyphae
  • medium name: ISP 3
  • further description: well-developed and branched substrate mycelium, no aerial mycelium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25195Bennett’s agaryes
25195ISP 2 agaryes
25195ISP 3yes
24852N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: 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

@refgrowthtypetemperaturerange
25195positivegrowth15-37
25195positiveoptimum28mesophilic
24852positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25195positivegrowth5.0-9.0alkaliphile
25195positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25195
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
25195non-motile, single, elliptical, smooth surface on substrate hyphaesporeyes
69481yes100
69480yes100

halophily

  • @ref: 25195
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-10(H2), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2519515824D-fructose-carbon source
2519516899D-mannitol-carbon source
2519517924D-sorbitol-carbon source
2519565327D-xylose-carbon source
2519515428glycine-nitrogen source
2519517268myo-inositol-carbon source
2519516977L-alanine-nitrogen source
2519530849L-arabinose-carbon source
2519518050L-glutamine-nitrogen source
2519562345L-rhamnose-carbon source
2519517115L-serine-nitrogen source
2519516857L-threonine-nitrogen source
2519517895L-tyrosine-nitrogen source
2519517632nitrate-reduction
2519516634raffinose-carbon source
2519528017starch-hydrolysis
2519553424tween 20-degradation
2519562968cellulose+degradation
2519516919creatine+nitrogen source
2519512936D-galactose+carbon source
2519517634D-glucose+carbon source
2519516024D-mannose+carbon source
2519516988D-ribose+carbon source
251954853esculin+hydrolysis
251955291gelatin+degradation
2519516467L-arginine+nitrogen source
2519517196L-asparagine+nitrogen source
2519529991L-aspartate+nitrogen source
2519529985L-glutamate+nitrogen source
2519517716lactose+carbon source
2519517306maltose+carbon source
25195skimmed milk+fermentation
2519517992sucrose+carbon source
2519553423tween 40+degradation
2519553426tween 80+degradation

metabolite production

  • @ref: 25195
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
25195catalase-1.11.1.6
25195urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2519510-methyl C18:01.7
    25195C15:0 anteiso11.4
    25195C15:012.6
    25195C16:1ω7c1.7
    25195C17:027
    25195C17:1ω7c10.7
    25195C18:08.1
    25195C18:1ω9c15
    25195C16:0 iso11.8
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 7
  • system: MIS MIDI
  • method/protocol: Xiang et al. 2011

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24852root of Parathelypteris beddomei (Bak.) ChingParathelypteris beddomeiHeilongjiang province, HarbinChinaCHNAsia44.206128.056
25195Gauseâ??s synthetic agar no. 1supplemented with cycloheximide (50 mg/l) and nalidixic acid (50 mg/l)2 weeks28
67770Root of Parathelypteris beddomei (Bak.) Ching from HarbinParathelypteris beddomeiHeilongjiang Province, north ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3471.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_3471&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: KU997023
  • Sequence Identity:
  • Total samples: 1419
  • soil counts: 1017
  • aquatic counts: 161
  • animal counts: 219
  • plant counts: 22

Safety information

risk assessment

  • @ref: 24852
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24852
  • description: Micromonospora parathelypteridis strain NEAU-JXY5 16S ribosomal RNA gene, partial sequence
  • accession: KU997023
  • length: 1507
  • database: ena
  • NCBI tax ID: 1839617

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora parathelypteridis CGMCC 4.7347GCA_014646315scaffoldncbi1839617
66792Micromonospora parathelypteridis DSM 103125GCA_014201145contigncbi1839617
66792Micromonospora parathelypteridis strain CGMCC 4.73471839617.4wgspatric1839617
66792Micromonospora parathelypteridis strain DSM 1031251839617.3wgspatric1839617
66792Micromonospora parathelypteridis DSM 1031252856470492draftimg1839617

GC content

@refGC-contentmethod
2519572.3Thermal denaturation, fluorometry
2485272.3thermal denaturation, midpoint method (Tm)
6777072-72.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.222no
gram-positiveyes89.945yes
anaerobicno99.417yes
aerobicyes95.361yes
halophileno94.79no
spore-formingyes93.931yes
thermophileno97.989yes
glucose-utilyes88.366yes
motileno91.338no
glucose-fermentno91.112no

External links

@ref: 24852

culture collection no.: DSM 103125, CGMCC 4.7347, JCM 32493

straininfo link

  • @ref: 91329
  • straininfo: 399121

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902235
  • title: Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching.
  • authors: Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001614
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptophyta/*microbiology
  • 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
24852Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103125Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103125)
25195S. L. Zhao, C.,Zheng, W.,Ma, Z.,Cao, T.,Zhao, J.,Yan, K.,Xiang, W.,Wang, X.Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching10.1099/ijsem.0.001614IJSEM 67: 268-274 201727902235
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/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
91329Reimer, 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-ID399121.1