Strain identifier
BacDive ID: 6175
Type strain:
Species: Dichotomicrobium thermohalophilum
Strain history: <- P. Hirsch and B. Hoffmann
NCBI tax ID(s): 933063 (species)
General
@ref: 1902
BacDive-ID: 6175
DSM-Number: 5002
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Dichotomicrobium thermohalophilum DSM 5002 is a thermophilic, Gram-negative bacterium that was isolated from solar lake.
NCBI tax id
- NCBI tax id: 933063
- Matching level: species
strain history
- @ref: 1902
- history: <- P. Hirsch and B. Hoffmann
doi: 10.13145/bacdive6175.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Hyphomicrobiaceae
- genus: Dichotomicrobium
- species: Dichotomicrobium thermohalophilum
- full scientific name: Dichotomicrobium thermohalophilum Hirsch and Hoffmann 1989
@ref: 1902
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Hyphomicrobiaceae
genus: Dichotomicrobium
species: Dichotomicrobium thermohalophilum
full scientific name: Dichotomicrobium thermohalophilum Hirsch and Hoffmann 1989
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
Culture and growth conditions
culture medium
- @ref: 1902
- name: DICHOTOMICROBIUM THERMOHALOPHILUM MEDIUM (DSMZ Medium 590)
- growth: yes
- link: https://mediadive.dsmz.de/medium/590
- composition: Name: DICHOTOMICROBIUM THERMOHALOPHILUM MEDIUM (DSMZ Medium 590) Composition: NaCl 69.0214 g/l MgCl2 x 6 H2O 31.2228 g/l Agar 18.0 g/l Na2SO4 11.515 g/l CaCl2 x 2 H2O 4.263 g/l NaHCO3 2.8224 g/l KCl 1.9502 g/l Yeast extract 1.0 g/l Na2-DL-malate 1.0 g/l MgSO4 x 7 H2O 0.594 g/l KBr 0.2842 g/l Nitrilotriacetic acid 0.2 g/l H3BO3 0.0784 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water
culture temp
- @ref: 1902
- growth: positive
- type: growth
- temperature: 43-45
- range: thermophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.979
Isolation, sampling and environmental information
isolation
- @ref: 1902
- sample type: solar lake
- geographic location: Sinai, Elat
- country: Israel
- origin.country: ISR
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Lake (large) |
#Condition | #Saline |
Safety information
risk assessment
- @ref: 1902
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Dichotomicrobium thermohalophilum partial 16S rRNA gene, type strain DSM5002T
- accession: FR733679
- length: 1469
- database: ena
- NCBI tax ID: 933063
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dichotomicrobium thermohalophilum DSM 5002 | GCA_003550175 | contig | ncbi | 933063 |
66792 | Dichotomicrobium thermohalophilum strain DSM 5002 | 933063.3 | wgs | patric | 933063 |
66792 | Dichotomicrobium thermohalophilum DSM 5002 | 2728369273 | draft | img | 933063 |
GC content
- @ref: 1902
- GC-content: 62.0-64.0
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 89 | no |
motile | no | 78.289 | no |
flagellated | no | 90.542 | no |
gram-positive | no | 98.066 | no |
anaerobic | no | 86.998 | no |
halophile | yes | 60.752 | no |
spore-forming | no | 94.422 | no |
glucose-util | yes | 64.636 | no |
aerobic | yes | 55.835 | no |
thermophile | yes | 68.239 | yes |
glucose-ferment | no | 93.406 | no |
External links
@ref: 1902
culture collection no.: DSM 5002, ATCC 49408, IFAM 954
straininfo link
- @ref: 75658
- straininfo: 45217
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1902 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5002) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5002 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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 | |
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) | |||
75658 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45217.1 | StrainInfo: A central database for resolving microbial strain identifiers |