Strain identifier

BacDive ID: 158370

Type strain: Yes

Species: Glycomyces dulcitolivorans

Strain Designation: SJ-25

Strain history: <- J. Zhao; Northeast Agricultural University, Harbin, P.R. CHINA; SJ-25<-J. Song; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing

NCBI tax ID(s): 2200759 (species)

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General

@ref: 65046

BacDive-ID: 158370

DSM-Number: 105121

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

description: Glycomyces dulcitolivorans SJ-25 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from rhizosphere soil of Triticum aestivum L..

NCBI tax id

  • NCBI tax id: 2200759
  • Matching level: species

strain history

  • @ref: 65046
  • history: <- J. Zhao; Northeast Agricultural University, Harbin, P.R. CHINA; SJ-25<-J. Song; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing

doi: 10.13145/bacdive158370.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Glycomycetales
  • family: Glycomycetaceae
  • genus: Glycomyces
  • species: Glycomyces dulcitolivorans
  • full scientific name: Glycomyces dulcitolivorans Mu et al. 2018

@ref: 65046

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Glycomycetaceae

genus: Glycomyces

species: Glycomyces dulcitolivorans

full scientific name: Glycomyces dulcitolivorans Mu et al. 2018

strain designation: SJ-25

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
66675positive
69480no93.6

colony morphology

  • @ref: 66675
  • colony color: white
  • incubation period: 28 days
  • medium used: ISP 3 agar

multimedia

  • @ref: 65046
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105121.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65046GYM 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
65046ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
65046STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
66675Bennett's agar mediayes
66675Czapek's agaryes
66675ISP 1yes
66675ISP 2yes
66675ISP 3yes
66675ISP 3 agaryes
66675ISP 4yes
66675ISP 6yes
66675Nutrient agar (NA)yes

culture temp

@refgrowthtypetemperature
65046positivegrowth28
66675positiveoptimum28
66675positivegrowth20-40

culture pH

@refabilitytypepHPH range
66675positiveoptimum7
66675positivegrowth4.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66675
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
66675straight or flexuous spores chains consisting of cylindrical sporessporeyes
69481yes100

halophily

  • @ref: 66675
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3.0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6667515824D-fructose-carbon source
6667516988D-ribose-carbon source
6667517716lactose-carbon source
6667517924D-sorbitol-carbon source
6667530849L-arabinose-carbon source
6667565327D-xylose-carbon source
6667512936D-galactose+carbon source
6667516024D-mannose+carbon source
6667516634raffinose+carbon source
6667516813galactitol+carbon source
6667516899D-mannitol+carbon source
6667517268myo-inositol+carbon source
6667517306maltose+carbon source
6667517634D-glucose+carbon source
6667517992sucrose+carbon source
6667562345L-rhamnose+carbon source
666755291gelatin+degradation
6667553423tween 40+degradation
6667553424tween 20+degradation
6667553426tween 80+degradation
6667562968cellulose+degradation
666754853esculin+hydrolysis
6667528017starch+hydrolysis
6667515428glycine-nitrogen source
6667517895L-tyrosine-nitrogen source
6667516467L-arginine+nitrogen source
6667516857L-threonine+nitrogen source
6667516919creatine+nitrogen source
6667516977L-alanine+nitrogen source
6667517115L-serine+nitrogen source
6667517196L-asparagine+nitrogen source
6667517203L-proline+nitrogen source
6667518050L-glutamine+nitrogen source
6667529985L-glutamate+nitrogen source
6667529991L-aspartate+nitrogen source
6667517632nitrate-reduction

metabolite production

  • @ref: 66675
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
66675urease-3.5.1.5
66675catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66675C17:0 iso1
    66675C14:0 iso10.1
    66675C17:0 anteiso10.5
    66675C15:0 iso11.7
    66675C18:02.5
    66675C15:0 anteiso25.2
    66675C16:0 iso28.2
    66675C16:1 w7c4.3
    66675C16:04.7
  • type of FA analysis: whole cell analysis
  • incubation medium: GY medium
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 7
  • library/peak naming table: NIST 14
  • method/protocol: Xiang et al. 2011

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
65046rhizosphere soil of Triticum aestivum L.Langfang, Hebei province (39° 32' N, 116° 40' E)ChinaCHNAsia39.5333116.667
66675rhizosphere soil of wheat (Triticum aestivum L.)Langfang, Hebei ProvinceChinaCHNAsia39.5333116.667humic acid-vitamin agarsupplemented with cycloheximide (50 mg l-1) and nalidixic acid (20 mg l-1)28 days28The rhizosphere soil sample was ground into powder and then suspended in sterile distilled water followed by a standard serial dilution technique. The diluted soil suspension was spread on humic acid-vitamin agar and incubated at 28°C for 28 days.

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 65046
  • description: Glycomyces dulcitolivorans strain SJ-25 16S ribosomal RNA gene, partial sequence
  • accession: MH342642
  • length: 1524
  • database: nuccore
  • NCBI tax ID: 2200759

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glycomyces dulcitolivorans SJ-25GCA_003265355scaffoldncbi2200759
66792Glycomyces dulcitolivorans SJ-252835077007draftimg2200759

GC content

  • @ref: 66675
  • GC-content: 72.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.895yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.669yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.082yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes82.361yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.909no
69480flagellatedmotile2+Ability to perform flagellated movementno93.6no

External links

@ref: 65046

culture collection no.: DSM 105121, CGMCC 4.7414

straininfo link

  • @ref: 111175
  • straininfo: 406549

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30063203Glycomyces dulcitolivorans sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.).Mu S, Sun T, Li Y, Jiang S, Guo X, Wang X, Zhao J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0029482018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny32242796Glycomyces albidus sp. nov., a novel actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.).Qian L, Duan L, Lin J, Yang Y, Song J, Wang X, Zhao J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0041312020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny33253081Glycomyces terrestris sp. nov., isolated from extremely arid soil from Yuanmou Earth Forest.Li Q, Li G, Lang L, An D, Jiang C, Jiang YInt J Syst Evol Microbiol10.1099/ijsem.0.0045802020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

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
65046Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105121Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105121)
66675Shan Mu, Tianyu Sun, Yuanyuan Li, Shanwen Jiang, Xiaowei Guo, Xiangjing Wang, Junwei Zhao, Wensheng XiangGlycomyces dulcitolivorans sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.)10.1099/ijsem.0.002948IJSEM 68: 3034-3039 201830063203
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
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
111175Reimer, 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-ID406549.1