Strain identifier
BacDive ID: 4240
Type strain:
Species: Dictyoglomus turgidum
Strain Designation: Z-1310
Strain history: <- V.A. Svetlichny, Z-1310
NCBI tax ID(s): 515635 (strain), 513050 (species)
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 id | Matching level |
---|---|
513050 | species |
515635 | strain |
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
@ref | gram stain | confidence |
---|---|---|
43415 | negative | |
69480 | negative | 99.922 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2790 | ANAEROCELLUM MEDIUM (DSMZ Medium 516) | yes | https://mediadive.dsmz.de/medium/516 | Name: 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 |
43415 | Terrific Broth | yes | 12g/L tryptone, 24g/L yeast extract, 9.4g/L K2HPO4, 2.2g/L KH2PO4, 4g/L glycerol |
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
2790 | positive | growth | 75 | thermophilic | |
43415 | positive | growth | 80 | hyperthermophilic | |
43415 | positive | optimum | 72 | thermophilic | |
69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
2790 | anaerobe | |
43415 | obligate anaerobe | |
69480 | anaerobe | 99.652 |
nutrition type
- @ref: 43415
- type: chemoorganotroph
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.922
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43415 | 16449 | alanine | + | degradation |
43415 | 22599 | arabinose | - | growth |
43415 | 22653 | asparagine | - | degradation |
43415 | 35391 | aspartate | - | degradation |
43415 | 85146 | carboxymethylcellulose | + | growth |
43415 | 62968 | cellulose | + | growth |
43415 | 15356 | cysteine | - | degradation |
43415 | 15428 | glycine | + | degradation |
43415 | 27570 | histidine | - | degradation |
43415 | 24898 | isoleucine | - | degradation |
43415 | 29985 | L-glutamate | + | degradation |
43415 | 25017 | leucine | - | degradation |
43415 | 6457 | lignin | + | growth |
43415 | 25094 | lysine | - | degradation |
43415 | 17309 | pectin | + | growth |
43415 | 28044 | phenylalanine | - | degradation |
43415 | 26271 | proline | - | degradation |
43415 | 17822 | serine | - | degradation |
43415 | 28017 | starch | + | growth |
43415 | 26986 | threonine | + | degradation |
43415 | 27897 | tryptophan | - | degradation |
43415 | 18186 | tyrosine | - | degradation |
43415 | 27266 | valine | - | degradation |
43415 | 18222 | xylose | - | growth |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
2790 | hot spring, Uzon volcano caldera | Kamchatka | Russia | RUS | Europe | ||
43415 | hot spring | Kamchatka, Uzon Caldera | Russia | RUS | Asia | 54 | 159 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dictyoglomus turgidum DSM 6724 | GCA_000021645 | complete | ncbi | 515635 |
66792 | Dictyoglomus turgidum DSM 6724 | 515635.4 | complete | patric | 515635 |
66792 | Dictyoglomus turgidum DSM 6724 | 643348543 | complete | img | 515635 |
GC content
@ref | GC-content | method |
---|---|---|
2790 | 32.5 | |
43415 | 33.96 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 85 | no |
motile | no | 84.558 | no |
flagellated | no | 98.213 | no |
gram-positive | no | 93.88 | no |
anaerobic | yes | 99.141 | yes |
aerobic | no | 98.09 | yes |
halophile | no | 90.769 | no |
spore-forming | no | 92.528 | no |
thermophile | yes | 100 | yes |
glucose-util | yes | 88.061 | no |
glucose-ferment | no | 71.732 | no |
External links
@ref: 2790
culture collection no.: DSM 6724
straininfo link
- @ref: 73737
- straininfo: 48279
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 24100573 | Expression, 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 LW | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309113024391 | 2013 | Bacteria/*enzymology, Bacterial Proteins/*chemistry, Carbohydrate Epimerases/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Histidine, Oligopeptides | |
Genetics | 28066333 | The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724 Reveals a Specialized Carbohydrate Fermentor. | Brumm PJ, Gowda K, Robb FT, Mead DA | Front Microbiol | 10.3389/fmicb.2016.01979 | 2016 | ||
Enzymology | 34379312 | Dictyoglomus 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 HA | Appl Biochem Biotechnol | 10.1007/s12010-021-03624-7 | 2021 | Bacteria/*enzymology, Bacterial Proteins/*chemistry, Hexoses/*chemical synthesis/chemistry, Phosphorylases/*chemistry | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2790 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6724) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6724 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
43415 | Phillip J. Brumm, Krishne Gowda, Frank T. Robb, David A. Mead | 10.3389/fmicb.2016.01979 | The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724 Reveals a Specialized Carbohydrate Fermentor | Front. Microbiol. 7: - 2016 | 28066333 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
73737 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48279.1 | StrainInfo: A central database for resolving microbial strain identifiers |