Strain identifier
BacDive ID: 5871
Type strain: 
Species: Halobaculum gomorrense
Strain Designation: DS2807
Strain history: DSM 9297 <-- A. Oren DS 2807.
NCBI tax ID(s): 43928 (species)
version 8.1 (current version)
General
@ref: 3535
BacDive-ID: 5871
DSM-Number: 9297
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative
description: Halobaculum gomorrense DS2807 is a mesophilic, Gram-negative archaeon of the family Halorubraceae.
NCBI tax id
- NCBI tax id: 43928
- Matching level: species
strain history
| @ref | history |
|---|---|
| 3535 | <- A. Oren, Hebrew Univ. Jerusalem, Israel, DS2807 |
| 67770 | DSM 9297 <-- A. Oren DS 2807. |
doi: 10.13145/bacdive5871.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Halorubraceae
- genus: Halobaculum
- species: Halobaculum gomorrense
- full scientific name: Halobaculum gomorrense Oren et al. 1995
@ref: 3535
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halorubraceae
genus: Halobaculum
species: Halobaculum gomorrense
full scientific name: Halobaculum gomorrense Oren et al. 1995
strain designation: DS2807
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.921
Culture and growth conditions
culture medium
- @ref: 3535
- name: HALOBACULUM GOMORRENSE MEDIUM (DSMZ Medium 823)
- growth: yes
- link: https://mediadive.dsmz.de/medium/823
- composition: Name: HALOBACULUM GOMORRENSE MEDIUM (DSMZ Medium 823) Composition: MgCl2 x 6 H2O 160.0 g/l NaCl 125.0 g/l K2SO4 5.0 g/l Starch 2.0 g/l Casamino acids 1.0 g/l Yeast extract 1.0 g/l CaCl2 x 2 H2O 0.1 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 3535 | positive | growth | 35 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.995 |
Isolation, sampling and environmental information
isolation
| @ref | geographic location | country | origin.country | continent | sample type |
|---|---|---|---|---|---|
| 3535 | Dead Sea | Israel | ISR | Asia | |
| 67770 | Dead Sea |
Safety information
risk assessment
- @ref: 3535
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnA | AB477982 | 1432 | ena | 43928 |
| 20218 | Halobaculum gomorrense gene for 16S ribosomal RNA, partial sequence, strain: JCM 9908, rrnB | AB477983 | 1432 | ena | 43928 |
| 20218 | Halobaculum gomorrense gene for 16S rRNA, complete sequence, strain: JCM 9908 | AB663364 | 1472 | ena | 43928 |
| 20218 | Halobaculum gomorrense strain JCM 9908 clone A 16S ribosomal RNA gene, partial sequence | HM159610 | 1472 | ena | 43928 |
| 20218 | Halobaculum gomorrense strain JCM 9908 clone B 16S ribosomal RNA gene, partial sequence | HM159611 | 1472 | ena | 43928 |
| 67770 | Halobaculum gomorrense 16S ribosomal RNA (16S rRNA) gene | L37444 | 1474 | ena | 43928 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halobaculum gomorrense DSM 9297 | 2695420988 | draft | img | 43928 |
| 67770 | Halobaculum gomorrense DSM 9297 | GCA_900129775 | scaffold | ncbi | 43928 |
| 66792 | Halobaculum gomorrense strain DSM 9297 | 43928.3 | wgs | patric | 43928 |
GC content
- @ref: 67770
- GC-content: 70
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 100
- training_data: no
External links
@ref: 3535
culture collection no.: DSM 9297, JCM 9908, ATCC 700876, CGMCC 1.10336
straininfo link
- @ref: 75351
- straininfo: 44189
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 7547294 | Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. | Oren A, Gurevich P, Gemmell RT, Teske A | Int J Syst Bacteriol | 10.1099/00207713-45-4-747 | 1995 | Archaea/*classification/genetics/metabolism, Base Composition, Base Sequence, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry/genetics | Genetics |
| Phylogeny | 20693359 | Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae. | Cui HL, Gao X, Yang X, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijs.0.026799-0 | 2010 | Base Composition, China, DNA, Archaeal/genetics, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Sodium Chloride, *Water Microbiology | Genetics |
| Phylogeny | 22611203 | Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. | Shimoshige H, Yamada T, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Usami R | Int J Syst Evol Microbiol | 10.1099/ijs.0.037432-0 | 2012 | Base Composition, Bolivia, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Japan, Magnesium/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylglycerols/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride | Genetics |
| Phylogeny | 28475027 | Halobaculum roseum sp. nov., isolated from underground salt deposits. | Chen S, Xu Y, Liu HC, Yang AN, Ke LX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001663 | 2017 | Base Composition, China, DNA, Archaeal/genetics, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Mining, Nucleic Acid Hybridization, Phosphatidylglycerols/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride | Transcriptome |
| Phylogeny | 35195509 | Halobaculum rubrum sp. nov., an extremely halophilic archaeon isolated from a salt lake. | Dilmurat M, Hu XY, Dilbar T, Cui HL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005242 | 2022 | China, DNA, Archaeal/genetics, *Halobacteriaceae/classification/isolation & purification, *Lakes/microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3535 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9297) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9297 | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 75351 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44189.1 | StrainInfo: A central database for resolving microbial strain identifiers |