Strain identifier

BacDive ID: 5841

Type strain: Yes

Species: Glycomyces arizonensis

Strain Designation: DPL-G-76

Strain history: DSM 44726 <-- NRRL B-16153 <-- D. P. Lebeda DPL-G-76.

NCBI tax ID(s): 1121926 (strain), 256035 (species)

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General

@ref: 12044

BacDive-ID: 5841

DSM-Number: 44726

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

description: Glycomyces arizonensis DPL-G-76 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil from kangaroo rat burrow.

NCBI tax id

NCBI tax idMatching level
256035species
1121926strain

strain history

@refhistory
12044<- D. P. Labeda, NRRL <- NCAUR; DPL-G-76
67770DSM 44726 <-- NRRL B-16153 <-- D. P. Lebeda DPL-G-76.

doi: 10.13145/bacdive5841.20230509.8.1

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 arizonensis
  • full scientific name: Glycomyces arizonensis Labeda and Kroppenstedt 2004

@ref: 12044

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Glycomycetaceae

genus: Glycomyces

species: Glycomyces arizonensis

full scientific name: Glycomyces arizonensis Labeda and Kroppenstedt 2004 emend. Nouioui et al. 2018

strain designation: DPL-G-76

type strain: yes

Morphology

cell morphology

@refgram staincell lengthmotilityconfidence
31227positive0.375 µm
69480no90.078
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19696Beige10-14 daysISP 2
19696Beige10-14 daysISP 3
1969610-14 daysISP 4
19696Beige10-14 daysISP 5
1969610-14 daysISP 6
19696Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19696noISP 2
19696yesISP 3Aerial MyceliumWhite
19696noISP 4
19696noISP 5
19696noISP 6
19696yesISP 7Aerial MyceliumWhite

pigmentation

  • @ref: 31227
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12044N-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
12044GYM 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
19696ISP 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
19696ISP 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:
19696ISP 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
19696ISP 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
19696ISP 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
19696ISP 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
19696positiveoptimum28mesophilic
12044positivegrowth28mesophilic
31227positivegrowth20-37
31227positiveoptimum28.5mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31227
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31227yes
69481yes100
69480no97.662

halophily

  • @ref: 31227
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H2), MK-10(H4), MK-11(H2), MK-11(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1969617234glucose+
1969622599arabinose+
1969617992sucrose+
1969618222xylose-
1969617268myo-inositol-
1969629864mannitol+
1969628757fructose+
1969626546rhamnose+
1969616634raffinose-
1969662968cellulose-
3122715963ribitol+carbon source
3122722599arabinose+carbon source
3122717057cellobiose+carbon source
3122723652dextrin+carbon source
3122728757fructose+carbon source
3122728260galactose+carbon source
3122717234glucose+carbon source
3122717754glycerol+carbon source
3122717716lactose+carbon source
3122717306maltose+carbon source
3122729864mannitol+carbon source
3122737684mannose+carbon source
3122717268myo-inositol+carbon source
3122726546rhamnose+carbon source
3122717814salicin+carbon source
3122730911sorbitol+carbon source
3122717992sucrose+carbon source
3122727082trehalose+carbon source
3122718222xylose+carbon source
312274853esculin+hydrolysis
3122717632nitrate+reduction

enzymes

@refvalueactivityec
31227catalase+1.11.1.6
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
19696+++-++-+-++++-++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
12044soil from kangaroo rat burrowArizonaUSAUSANorth America
67770Soil from a kangaroo rat (Dipodomys sp.) burrowAZUSAUSANorth AmericaDipodomys sp.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Mammals#Rodentia (Other)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7558.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_344;96_1445;97_4328;98_5540;99_7558&stattab=map
  • Last taxonomy: Glycomyces arizonensis subclade
  • 16S sequence: AY462042
  • Sequence Identity:
  • Total samples: 321
  • soil counts: 113
  • aquatic counts: 16
  • animal counts: 129
  • plant counts: 63

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120441Risk group (German classification)
196961Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12044
  • description: Glycomyces arizonensis 16S ribosomal RNA gene, partial sequence
  • accession: AY462042
  • length: 1499
  • database: ena
  • NCBI tax ID: 256035

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glycomyces arizonensis DSM 447261121926.3wgspatric1121926
66792Glycomyces arizonensis DSM 447262523533535draftimg1121926
67770Glycomyces arizonensis DSM 44726GCA_000482705scaffoldncbi1121926

GC content

  • @ref: 67770
  • GC-content: 70.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.788no
flagellatedno97.63no
gram-positiveyes91.702yes
anaerobicno98.862yes
halophileno71.24no
spore-formingyes92.725yes
thermophileno90.107no
glucose-utilyes87.523yes
aerobicyes90.737yes
glucose-fermentno86.511no

External links

@ref: 12044

culture collection no.: DSM 44726, JCM 14911, NRRL B-16153, NBRC 103886

straininfo link

  • @ref: 75322
  • straininfo: 132660

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545481Emended description of the genus Glycomyces and description of Glycomyces algeriensis sp. nov., Glycomyces arizonensis sp. nov. and Glycomyces lechevalierae sp. nov.Labeda DP, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.63089-02004Actinomycetales/chemistry/*classification/cytology/genetics, Bacterial Typing Techniques, Carbohydrates/analysis/isolation & purification, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny24736858Glycomyces phytohabitans sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte in Jiangsu, East China.Xing K, Qin S, Zhang WD, Cao CL, Ruan JS, Huang Y, Jiang JHJ Antibiot (Tokyo)10.1038/ja.2014.402014Actinobacteria/classification/*genetics/*isolation & purification, Asteraceae/*microbiology, China, Phylogeny, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiologyEnzymology
Phylogeny25713037Glycomyces tarimensis sp. nov., an actinomycete isolated from a saline-alkali habitat.Lv LL, Zhang YF, Zhang LLInt J Syst Evol Microbiol10.1099/ijs.0.0001432015Actinomycetales/*classification/genetics/isolation & purification, Alkalies, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12044Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44726)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44726
19696Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44726.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
31227Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2755328776041
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75322Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132660.1StrainInfo: A central database for resolving microbial strain identifiers