Strain identifier

BacDive ID: 5833

Type strain: Yes

Species: Glycomyces rutgersensis

Strain history: DSM 43812 <-- NRRL B-16106 <-- D. P. Labeda et al. LL-I-20.

NCBI tax ID(s): 58115 (species)

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General

@ref: 11285

BacDive-ID: 5833

DSM-Number: 43812

keywords: 16S sequence, Bacteria

description: Glycomyces rutgersensis DSM 43812 is a bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 58115
  • Matching level: species

strain history

@refhistory
11285<- NRRL
67770DSM 43812 <-- NRRL B-16106 <-- D. P. Labeda et al. LL-I-20.

doi: 10.13145/bacdive5833.20240510.9

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

@ref: 11285

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Glycomycetaceae

genus: Glycomyces

species: Glycomyces rutgersensis

full scientific name: Glycomyces rutgersensis Labeda et al. 1985

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19594Beige10-14 daysISP 2
1959410-14 daysISP 3
19594Beige10-14 daysISP 4
1959410-14 daysISP 5
19594Beige10-14 daysISP 6
1959410-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19594noISP 2
19594noISP 3
19594yesISP 4Aerial MyceliumWhite
19594noISP 5
19594noISP 6
19594noISP 7

multimedia

  • @ref: 11285
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43812.jpg
  • caption: Medium 65 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19594ISP 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
19594ISP 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:
19594ISP 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
19594ISP 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
19594ISP 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
19594ISP 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
11285GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65

culture temp

@refgrowthtypetemperature
11285positivegrowth37
67770positivegrowth30

Physiology and metabolism

halophily

  • @ref: 19594
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
19594+++----+-+-++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19594------+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11285soilChinaCHNAsia
67770Greenhouse soilUSAUSANorth AmericaTrenton, NJ

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_168704.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_344;96_3110;97_3811;98_10147;99_168704&stattab=map
  • Last taxonomy: Glycomyces
  • 16S sequence: AJ293748
  • Sequence Identity:
  • Total samples: 777
  • soil counts: 588
  • aquatic counts: 25
  • animal counts: 39
  • plant counts: 125

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
195941Risk group (German classification)
112851Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Glycomyces rutgersensis gene for 16S ribosomal RNA, partial sequenceD854841487nuccore58115
20218Glycomyces rutgersensis partial 16S rRNA gene, strain IMSNU 22074TAJ2937481522nuccore58115

GC content

@refGC-contentmethod
6777070Buoyant density centrifugation (BD)
6777073thermal denaturation, midpoint method (Tm)

External links

@ref: 11285

culture collection no.: DSM 43812, ATCC 43156, NRRL B-16106, JCM 6238, CGMCC 4.1363, IFO 14488, IFO 15934, IMET 43813, IMSNU 22074, KCTC 9654, NBRC 14488, NBRC 15934, VKM Ac-1248

straininfo link

  • @ref: 75315
  • straininfo: 88640

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny30465323Glycomyces luteolus sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.).Duan L, Song W, Jiang S, Qian L, Guo X, Wang X, Zhao J, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-018-1200-z2018Actinobacteria/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Soil/chemistry, *Soil Microbiology, Triticum/growth & developmentMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11285Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43812)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43812
19594Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43812.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
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
75315Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88640.1StrainInfo: A central database for resolving microbial strain identifiers