Strain identifier
BacDive ID: 5983
Type strain: 
Species: Halobacteroides halobius
Strain Designation: MD-1
Strain history: <- ATCC <- A. Oren, MD-1
NCBI tax ID(s): 748449 (strain), 42422 (species)
version 8.1 (current version)
General
@ref: 1932
BacDive-ID: 5983
DSM-Number: 5150
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Halobacteroides halobius MD-1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 42422 | species |
| 748449 | strain |
strain history
- @ref: 1932
- history: <- ATCC <- A. Oren, MD-1
doi: 10.13145/bacdive5983.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Halanaerobiales
- family: Halobacteroidaceae
- genus: Halobacteroides
- species: Halobacteroides halobius
- full scientific name: Halobacteroides halobius Oren et al. 1984
@ref: 1932
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Halanaerobiales
family: Halobacteroidaceae
genus: Halobacteroides
species: Halobacteroides halobius
full scientific name: Halobacteroides halobius Oren et al. 1984
strain designation: MD-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- motility: yes
- confidence: 91.012
multimedia
- @ref: 66793
- multimedia content: EM_DSM_5150_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1932
- name: HALOBACTEROIDES HALOBIUS MEDIUM (DSMZ Medium 588)
- growth: yes
- link: https://mediadive.dsmz.de/medium/588
- composition: Name: HALOBACTEROIDES HALOBIUS MEDIUM (DSMZ Medium 588) Composition: NaCl 87.8 g/l MgCl2 x 6 H2O 20.3 g/l PIPES 12.096 g/l CaCl2 x 2 H2O 7.35 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l KCl 3.7 g/l L-Cysteine HCl x H2O 0.5 g/l Resazurin 0.0001 g/l Distilled water
culture temp
- @ref: 1932
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.999
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 98.943 |
Isolation, sampling and environmental information
isolation
- @ref: 1932
- sample type: sediment
- geographic location: Dead Sea
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
Safety information
risk assessment
- @ref: 1932
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halobacteroides halobius 16S ribosomal RNA gene | U32595 | 1505 | ena | 748449 |
| 20218 | H.halobius gene for 16S ribosomal RNA | X89074 | 1471 | ena | 748449 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halobacteroides halobius DSM 5150 | GCA_000328625 | complete | ncbi | 748449 |
| 66792 | Halobacteroides halobius DSM 5150 | 748449.3 | complete | patric | 748449 |
| 66792 | Halobacteroides halobius DSM 5150 | 2509601017 | complete | img | 748449 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 86.526 | no |
| flagellated | no | 60.241 | no |
| gram-positive | no | 86.557 | no |
| anaerobic | yes | 95.033 | no |
| aerobic | no | 96.87 | no |
| halophile | no | 67.656 | no |
| spore-forming | no | 54.455 | no |
| thermophile | yes | 54.954 | yes |
| glucose-util | yes | 85.371 | no |
| glucose-ferment | yes | 50.678 | no |
External links
@ref: 1932
culture collection no.: DSM 5150, ATCC 35273
straininfo link
- @ref: 75472
- straininfo: 40963
literature
- topic: Phylogeny
- Pubmed-ID: 21761211
- title: Characterization of Halanaerocella petrolearia gen. nov., sp. nov., a new anaerobic moderately halophilic fermentative bacterium isolated from a deep subsurface hypersaline oil reservoir : New taxa: Firmicutes (Class Clostridia, Order Halanaerobiales, Halobacteroidaceae, Halobacteroides).
- authors: Gales G, Chehider N, Joulian C, Battaglia-Brunet F, Cayol JL, Postec A, Borgomano J, Neria-Gonzalez I, Lomans BP, Ollivier B, Alazard D
- journal: Extremophiles
- DOI: 10.1007/s00792-011-0387-y
- year: 2011
- mesh: Anaerobiosis/physiology, Base Sequence, Carbohydrate Metabolism/*physiology, Genotype, Gram-Positive Endospore-Forming Bacteria/cytology/*genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, *Phylogeny, Salinity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1932 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5150) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5150 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 75472 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40963.1 | StrainInfo: A central database for resolving microbial strain identifiers |