Strain identifier

BacDive ID: 5835

Type strain: Yes

Species: Glycomyces harbinensis

Strain Designation: LL-D05139, LL-DO 5139

Strain history: IMET 43812 <-- IFO 14487 <-- NRRL 15337 <-- D. P. Labeda et al. LL-D05139.

NCBI tax ID(s): 58114 (species)

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General

@ref: 12581

BacDive-ID: 5835

DSM-Number: 46494

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

description: Glycomyces harbinensis LL-D05139 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 58114
  • Matching level: species

strain history

@refhistory
12581<- IMET <- IFO <- NRRL <- M.P. Lechevalier, LL-DO 5139
67770IMET 43812 <-- IFO 14487 <-- NRRL 15337 <-- D. P. Labeda et al. LL-D05139.

doi: 10.13145/bacdive5835.20230509.8.1

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 harbinensis
  • full scientific name: Glycomyces harbinensis Labeda et al. 1985

@ref: 12581

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Glycomycetaceae

genus: Glycomyces

species: Glycomyces harbinensis

full scientific name: Glycomyces harbinensis Labeda et al. 1985

strain designation: LL-D05139, LL-DO 5139

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
20196Ivory (1014)10-14 daysISP 2
20196Ivory (1014)10-14 daysISP 3
20196Ivory (1014)10-14 daysISP 4
20196Ivory (1014)10-14 daysISP 5
20196Ivory (1014)10-14 daysISP 6
20196Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20196noISP 2
20196noISP 3
20196yesISP 4Aerial MyceliumWhite
20196yesISP 5Aerial MyceliumWhite
20196noISP 6
20196yesISP 7Aerial MyceliumWhite

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
20196ISP 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
20196ISP 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:
20196ISP 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
20196ISP 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
20196ISP 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
20196ISP 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
12581GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
12581GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf

culture temp

@refgrowthtypetemperaturerange
12581positivegrowth28mesophilic
20196positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 98.687

compound production

@refcompound
12581antibiotic DO5139 ß
20196N-L-Alanyl-L-serine diazoacetate

halophily

  • @ref: 20196
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2019617234glucose+
2019622599arabinose+
2019617992sucrose+
2019618222xylose-
2019617268myo-inositol-
2019629864mannitol+
2019628757fructose+
2019626546rhamnose+
2019616634raffinose-
2019662968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
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
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20196+++-++-+++-++-++-+-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20196++--+----++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
12581soilChinaCHNAsia
67770SoilChinaCHNAsiaHarbin

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_13416.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_344;96_3110;97_3811;98_10147;99_13416&stattab=map
  • Last taxonomy: Glycomyces harbinensis
  • 16S sequence: AJ293747
  • Sequence Identity:
  • Total samples: 670
  • soil counts: 373
  • aquatic counts: 7
  • animal counts: 14
  • plant counts: 276

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
125811Risk group (German classification)
201961German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Glycomyces harbinensis gene for 16S ribosomal RNA, partial sequenceD854831487ena58114
67770Glycomyces harbinensis partial 16S rRNA gene, strain IMSNU 20070TAJ2937471525ena58114

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glycomyces harbinensis strain CGMCC 4.351658114.3wgspatric58114
66792Glycomyces harbinensis CGMCC 4.35162663762751draftimg58114
67770Glycomyces harbinensis CGMCC 4.3516GCA_900101745scaffoldncbi58114

GC content

@refGC-contentmethod
1258171.0
6777071thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes84no
gram-positiveyes93.308no
anaerobicno99.041no
halophileno56.522no
spore-formingyes90.961no
glucose-utilyes87.047no
thermophileno97.829yes
flagellatedno97.764no
motileno92.261no
aerobicyes91.506no
glucose-fermentno88.079no

External links

@ref: 12581

culture collection no.: DSM 46494, ATCC 43155, IAM 14283, IFO 14487, IMET 43812, JCM 7347, NBRC 14487, NRRL 15337, BCRC 16361, CGMCC 4.1364, CGMCC 4.3516, IMSNU 20070, KCTC 9362, KCTC 9655, NCIMB 13371, VKM Ac-1247

straininfo link

  • @ref: 75317
  • straininfo: 41680

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny3429335New antitumor antibiotic, LL-D05139 beta. Fermentation, isolation, structure determination and biological activities.Lee MD, Fantini AA, Kuck NA, Greenstein M, Testa RT, Borders DBJ Antibiot (Tokyo)10.7164/antibiotics.40.16571987*Antibiotics, Antineoplastic/isolation & purification/pharmacology, Azaserine/*analogs & derivatives/biosynthesis/isolation & purification, DNA Damage, Fermentation, Fungi/*analysis, Magnetic Resonance Spectroscopy, Microbial Sensitivity Tests, Soil Microbiology, Spectrophotometry, Infrared, Spectrophotometry, UltravioletEnzymology
Phylogeny18984687Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees.Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.2008/000398-02008Actinomycetales/*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 SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46494)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46494
20196Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM46494.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
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
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75317Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41680.1StrainInfo: A central database for resolving microbial strain identifiers