Strain identifier
BacDive ID: 134076
Type strain: 
Species: Halosimplex rubrum
Strain Designation: R27
Strain history: H.-L. Cui; Jiangsu Univ., China; R27.
NCBI tax ID(s): 869889 (species)
version 9.3 (current version)
General
@ref: 31179
BacDive-ID: 134076
keywords: genome sequence, 16S sequence, Archaea, aerobe, Gram-negative, motile
description: Halosimplex rubrum R27 is an aerobe, Gram-negative, motile archaeon that was isolated from salted brown alga.
NCBI tax id
- NCBI tax id: 869889
- Matching level: species
strain history
- @ref: 67770
- history: H.-L. Cui; Jiangsu Univ., China; R27.
doi: 10.13145/bacdive134076.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Haloarculaceae
- genus: Halosimplex
- species: Halosimplex rubrum
- full scientific name: Halosimplex rubrum Han and Cui 2014
@ref: 31179
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloarculaceae
genus: Halosimplex
species: Halosimplex rubrum
strain designation: R27
type strain: yes
Morphology
cell morphology
- @ref: 31179
- gram stain: negative
- motility: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 31179 | positive | growth | 25-45 |
| 31179 | positive | optimum | 42 |
| 67770 | positive | growth | 37 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31179 | positive | growth | 5.5-9.5 | alkaliphile |
| 31179 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31179
- oxygen tolerance: aerobe
spore formation
- @ref: 125439
- spore formation: no
- confidence: 93.3
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31179 | NaCl | positive | growth | 0.9-3.4 % |
| 31179 | NaCl | positive | optimum | 3.1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31179 | 35391 | aspartate | + | carbon source |
| 31179 | 28260 | galactose | + | carbon source |
| 31179 | 17234 | glucose | + | carbon source |
| 31179 | 29987 | glutamate | + | carbon source |
| 31179 | 24996 | lactate | + | carbon source |
| 31179 | 29864 | mannitol | + | carbon source |
| 31179 | 37684 | mannose | + | carbon source |
| 31179 | 18257 | ornithine | + | carbon source |
| 31179 | 30911 | sorbitol | + | carbon source |
| 31179 | 17992 | sucrose | + | carbon source |
metabolite production
- @ref: 31179
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 31179 | salted brown alga | |||||
| 67770 | Salted brown alga Laminaria produced at Dalian | Laminaria | Liaoning Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Algae | #Brown Algae |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_188934.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17860;96_69458;97_90218;98_122624;99_188934&stattab=map
- Last taxonomy: Halosimplex
- 16S sequence: HM159603
- Sequence Identity:
- Total samples: 2
- aquatic counts: 2
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Halosimplex rubrum strain R27 16S ribosomal RNA gene, partial sequence | HM159603 | 1473 | nuccore | 869889 |
| 67770 | Halosimplex rubrum strain R27 16S ribosomal RNA (rrnB) gene, partial sequence | KF434757 | 1473 | nuccore | 869889 |
Genome sequences
- @ref: 66792
- description: Halosimplex rubrum R27
- accession: GCA_013415885
- assembly level: complete
- database: ncbi
- NCBI tax ID: 869889
GC content
| @ref | GC-content | method |
|---|---|---|
| 31179 | 64 | |
| 67770 | 64 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 72.97 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 81.925 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 78.68 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.231 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 79.02 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 86.529 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 93.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 58.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 87.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate anaerobe | 81.4 |
External links
@ref: 31179
culture collection no.: CGMCC 1.10591, JCM 17268
literature
- topic: Phylogeny
- Pubmed-ID: 24048865
- title: Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov., isolated from salted brown alga Laminaria, and emended description of the genus Halosimplex.
- authors: Han D, Cui HL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.056887-0
- year: 2013
- mesh: Base Composition, China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Laminaria/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 31179 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27506 | 28776041 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | ||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |