Strain identifier

BacDive ID: 5843

Type strain: Yes

Species: Glycomyces endophyticus

Culture col. no.: DSM 45002, JCM 16001, KCTC 19152, YIM 56134

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12234

BacDive-ID: 5843

DSM-Number: 45002

keywords: mesophilic, spore-forming, aerobe, Bacteria, 16S sequence, gram-positive, rod-shaped

description: Glycomyces endophyticus DSM 45002 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from surface-sterilized root of Carex baccans Nees collected from tropical rainforest.

strain history: <- S.-K. Tang; YIM 56134 <- H.-H. Chen

doi: 10.13145/bacdive5843.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinobacteria
  • domain: Bacteria
  • phylum: Actinobacteria
  • class: Actinobacteria
  • order: Glycomycetales
  • family: Glycomycetaceae
  • genus: Glycomyces
  • species: Glycomyces endophyticus
  • full scientific name: Glycomyces endophyticus Qin et al. 2008

@ref: 12234

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Glycomycetaceae

genus: Glycomyces

species: Glycomyces endophyticus

full scientific name: Glycomyces endophyticus Qin et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 31187
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19714Saffron yellow10-14 daysISP 2
1971410-14 daysISP 3
19714Saffron yellow10-14 daysISP 4
19714Beige10-14 daysISP 5
19714Saffron yellow10-14 daysISP 6
19714Ochre brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
19714yesAerial MyceliumISP 2
19714yesAerial MyceliumISP 3Cream
19714yesAerial MyceliumISP 4Cream
19714yesAerial MyceliumISP 5Cream
19714noISP 6
19714yesAerial MyceliumISP 7Cream

pigmentation

  • @ref: 31187
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12234GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
19714ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19714ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19714ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19714ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19714ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19714ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
19714positiveoptimum28mesophilic
12234positivegrowth28mesophilic
31187positivegrowth15-37
31187positiveoptimum28mesophilic

culture pH

@refabilitytypepH
31187positivegrowth7
31187positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31187
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31187
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31187NaClpositivegrowth0-5 %
31187NaClpositiveoptimum0-5 %

observation

  • @ref: 31187
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3118717272propionate+carbon source
3118730031succinate+carbon source
311874853esculin+hydrolysis

enzymes

  • @ref: 31187
  • value: urease
  • activity: +
  • ec: 3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19714+++++--++++++-++-++

Isolation, sampling and environmental information

isolation

  • @ref: 12234
  • sample type: surface-sterilized root of Carex baccans Nees collected from tropical rainforest
  • host species: Carex baccans
  • geographic location: Xishuangbanna, Yunnan Province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 12234
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12234
  • description: Glycomyces endophyticus strain YIM 56134 16S ribosomal RNA gene, partial sequence
  • accession: EU200681
  • length: 1456
  • database: ena
  • NCBI tax ID: 480996

GC content

@refGC-contentmethod
1223472.0high performance liquid chromatography (HPLC)
3118772

External links

@ref: 12234

culture collection no.: DSM 45002, JCM 16001, KCTC 19152, YIM 56134

straininfo link

@refpassport
20218http://www.straininfo.net/strains/690819
20218http://www.straininfo.net/strains/856448
20218http://www.straininfo.net/strains/835994
20218http://www.straininfo.net/strains/690820

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12234Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45002
19714Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45002.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2751410.1099/ijs.0.2008/000398-0
31187Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information27514