Strain identifier

BacDive ID: 4240

Type strain: Yes

Species: Dictyoglomus turgidum

Strain Designation: Z-1310

Strain history: <- V.A. Svetlichny, Z-1310

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

@ref: 2790

BacDive-ID: 4240

DSM-Number: 6724

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemoorganotroph, thermophilic, Gram-negative

description: Dictyoglomus turgidum Z-1310 is an anaerobe, chemoorganotroph, thermophilic bacterium that was isolated from hot spring, Uzon volcano caldera.

NCBI tax id

NCBI tax idMatching level
513050species
515635strain

strain history

  • @ref: 2790
  • history: <- V.A. Svetlichny, Z-1310

doi: 10.13145/bacdive4240.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/dictyoglomerota
  • domain: Bacteria
  • phylum: Dictyoglomerota
  • class: Dictyoglomeria
  • order: Dictyoglomerales
  • family: Dictyoglomeraceae
  • genus: Dictyoglomus
  • species: Dictyoglomus turgidum
  • full scientific name: Dictyoglomus turgidum corrig. Svetlichny and Svetlichnayá 1995
  • synonyms

    • @ref: 20215
    • synonym: Dictyoglomus turgidus

@ref: 2790

domain: Bacteria

phylum: Dictyoglomi

class: Dictyoglomia

order: Dictyoglomales

family: Dictyoglomaceae

genus: Dictyoglomus

species: Dictyoglomus turgidum

full scientific name: Dictyoglomus turgidum Svetlichny and Svetlichnayá 1995

strain designation: Z-1310

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
43415negative
69480negative99.922

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2790ANAEROCELLUM MEDIUM (DSMZ Medium 516)yeshttps://mediadive.dsmz.de/medium/516Name: ANAEROCELLUM MEDIUM (DSMZ Medium 516; with strain-specific modifications) Composition: Starch 4.99002 g/l Na2CO3 1.49701 g/l Yeast extract 0.499002 g/l Na2S x 9 H2O 0.499002 g/l CaCl2 x 2 H2O 0.329341 g/l MgCl2 x 6 H2O 0.329341 g/l KCl 0.329341 g/l KH2PO4 0.329341 g/l NH4Cl 0.329341 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water
43415Terrific Brothyes12g/L tryptone, 24g/L yeast extract, 9.4g/L K2HPO4, 2.2g/L KH2PO4, 4g/L glycerol

culture temp

@refgrowthtypetemperaturerangeconfidence
2790positivegrowth75thermophilic
43415positivegrowth80hyperthermophilic
43415positiveoptimum72thermophilic
69480thermophilic100

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2790anaerobe
43415obligate anaerobe
69480anaerobe99.652

nutrition type

  • @ref: 43415
  • type: chemoorganotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.922

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4341516449alanine+degradation
4341522599arabinose-growth
4341522653asparagine-degradation
4341535391aspartate-degradation
4341585146carboxymethylcellulose+growth
4341562968cellulose+growth
4341515356cysteine-degradation
4341515428glycine+degradation
4341527570histidine-degradation
4341524898isoleucine-degradation
4341529985L-glutamate+degradation
4341525017leucine-degradation
434156457lignin+growth
4341525094lysine-degradation
4341517309pectin+growth
4341528044phenylalanine-degradation
4341526271proline-degradation
4341517822serine-degradation
4341528017starch+growth
4341526986threonine+degradation
4341527897tryptophan-degradation
4341518186tyrosine-degradation
4341527266valine-degradation
4341518222xylose-growth

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
2790hot spring, Uzon volcano calderaKamchatkaRussiaRUSEurope
43415hot springKamchatka, Uzon CalderaRussiaRUSAsia54159

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Environmental#Terrestrial#Volcanic
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3207.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_379;96_1669;97_1998;98_2458;99_3207&stattab=map
  • Last taxonomy: Dictyoglomus turgidum
  • 16S sequence: NR_074885
  • Sequence Identity:
  • Total samples: 48
  • soil counts: 1
  • aquatic counts: 46
  • animal counts: 1

Safety information

risk assessment

  • @ref: 2790
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 43415
  • description: 16S rRNA gene sequence
  • accession: NR_074885
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dictyoglomus turgidum DSM 6724GCA_000021645completencbi515635
66792Dictyoglomus turgidum DSM 6724515635.4completepatric515635
66792Dictyoglomus turgidum DSM 6724643348543completeimg515635

GC content

@refGC-contentmethod
279032.5
4341533.96genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes85no
motileno84.558no
flagellatedno98.213no
gram-positiveno93.88no
anaerobicyes99.141yes
aerobicno98.09yes
halophileno90.769no
spore-formingno92.528no
thermophileyes100yes
glucose-utilyes88.061no
glucose-fermentno71.732no

External links

@ref: 2790

culture collection no.: DSM 6724

straininfo link

  • @ref: 73737
  • straininfo: 48279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology24100573Expression, crystallization and preliminary X-ray crystallographic analysis of cellobiose 2-epimerase from Dictyoglomus turgidum DSM 6724.Pham TV, Hong SH, Hong MK, Ngo HP, Oh DK, Kang LWActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091130243912013Bacteria/*enzymology, Bacterial Proteins/*chemistry, Carbohydrate Epimerases/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Histidine, Oligopeptides
Genetics28066333The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724 Reveals a Specialized Carbohydrate Fermentor.Brumm PJ, Gowda K, Robb FT, Mead DAFront Microbiol10.3389/fmicb.2016.019792016
Enzymology34379312Dictyoglomus turgidum DSM 6724 alpha-Glucan Phosphorylase: Characterization and Its Application in Multi-enzyme Cascade Reaction for D-Tagatose Production.Dai Y, Zhang T, Jiang B, Mu W, Chen J, Hassanin HAAppl Biochem Biotechnol10.1007/s12010-021-03624-72021Bacteria/*enzymology, Bacterial Proteins/*chemistry, Hexoses/*chemical synthesis/chemistry, Phosphorylases/*chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2790Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6724)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6724
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
43415Phillip J. Brumm, Krishne Gowda, Frank T. Robb, David A. Mead10.3389/fmicb.2016.01979The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724 Reveals a Specialized Carbohydrate FermentorFront. Microbiol. 7: - 201628066333
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
73737Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48279.1StrainInfo: A central database for resolving microbial strain identifiers