Strain identifier

BacDive ID: 5843

Type strain: Yes

Species: Glycomyces endophyticus

Strain history: <- S-K Tang, Yunnan Inst. Microbiol, China

NCBI tax ID(s): 480996 (species)

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General

@ref: 12234

BacDive-ID: 5843

DSM-Number: 45002

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

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

NCBI tax id

  • NCBI tax id: 480996
  • Matching level: species

strain history

@refhistory
12234<- S.-K. Tang; YIM 56134 <- H.-H. Chen
67770DSM 45002 <-- S.-K. Tang YIM 56134 <-- H.-H. Chen.
67771<- S-K Tang, Yunnan Inst. Microbiol, China

doi: 10.13145/bacdive5843.20240510.9

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 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

@refgram staincell shape
31187positiverod-shaped
67771positive

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://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
12234GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.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

@refgrowthtypetemperature
19714positiveoptimum28
12234positivegrowth28
31187positivegrowth15-37
31187positiveoptimum28
67770positivegrowth28
67771positivegrowth28

culture pH

@refabilitytypepH
31187positivegrowth7
31187positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31187aerobe
67771aerobe

spore formation

  • @ref: 31187
  • spore formation: yes

halophily

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

observation

@refobservation
31187aggregates in chains
67770quinones: MK-10(H4), MK-11(H4)

metabolite utilization

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

enzymes

@refvalueactivityec
31187urease+3.5.1.5
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1

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

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12234surface-sterilized root of Carex baccans Nees collected from tropical rainforestCarex baccansXishuangbanna, Yunnan ProvinceChinaCHNAsia
67770Surface-sterilized root of Carex baccans from a tropical rainforestCarex baccansXishuangbanna, Yunnan ProvinceChinaCHNAsia
67771From plantYunnan ProvinceChinaCHNAsia

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: nuccore
  • NCBI tax ID: 480996

GC content

@refGC-contentmethod
1223472.0high performance liquid chromatography (HPLC)
3118772
6777072high performance liquid chromatography (HPLC)

External links

@ref: 12234

culture collection no.: DSM 45002, JCM 16001, KCTC 19152, YIM 56134, NBRC 107830

straininfo link

  • @ref: 75324
  • straininfo: 297479

literature

  • topic: Phylogeny
  • Pubmed-ID: 18984687
  • title: Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees.
  • authors: Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL, Xu LH, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/000398-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Carex Plant/*microbiology, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
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
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31187Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2751428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
75324Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297479.1StrainInfo: A central database for resolving microbial strain identifiers