Strain identifier
BacDive ID: 4285
Type strain: 
Species: Halorhodospira neutriphila
Strain history: A. Hirschler-Réa SG 3301.
NCBI tax ID(s): 168379 (species)
version 9.1 (current version)
General
@ref: 5718
BacDive-ID: 4285
DSM-Number: 15116
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Halorhodospira neutriphila DSM 15116 is an anaerobe, Gram-negative bacterium that was isolated from microbial mat in marine saltern.
NCBI tax id
- NCBI tax id: 168379
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5718 | <- P. Caumette; SG3301 <- R. Matheron |
| 67770 | A. Hirschler-Réa SG 3301. |
doi: 10.13145/bacdive4285.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Halorhodospiraceae
- genus: Halorhodospira
- species: Halorhodospira neutriphila
- full scientific name: Halorhodospira neutriphila Hirschler-Réa et al. 2003
@ref: 5718
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Halorhodospira
species: Halorhodospira neutriphila
full scientific name: Halorhodospira neutriphila Hirschler-Réa et al. 2003
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.75
Culture and growth conditions
culture medium
- @ref: 5718
- name: HALORHODOSPIRA MEDIUM (DSMZ Medium 999)
- growth: yes
- link: https://mediadive.dsmz.de/medium/999
- composition: Name: HALORHODOSPIRA MEDIUM (DSMZ Medium 999) Composition: NaCl 100.0 g/l NaHCO3 2.0 g/l MgCl2 x 6 H2O 2.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l Na2S x 9 H2O 0.75 g/l NH4Cl 0.5 g/l CaCl2 x 2 H2O 0.05 g/l FeSO4 x 7 H2O 0.0011 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l Pyridoxamine 5e-05 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Vitamine B12 2e-05 g/l Nicotinate 2e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l p-Aminobenzoate 1e-05 g/l Thiamine 1e-05 g/l Pantothenate 5e-06 g/l Biotine 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 5718 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 5718
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 90.847 |
| 69481 | no | 94 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5718 | microbial mat in marine saltern | Rhone Delta | France | FRA | Europe |
| 67770 | Microbial mat in marine saltern |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Microbial community | #Microbial mat |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_107629.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15363;96_43192;97_55268;98_73146;99_107629&stattab=map
- Last taxonomy: Halorhodospira neutriphila subclade
- 16S sequence: AJ318525
- Sequence Identity:
- Total samples: 109
- soil counts: 7
- aquatic counts: 87
- animal counts: 13
- plant counts: 2
Safety information
risk assessment
- @ref: 5718
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halorhodospira neutriphila gene for 16S ribosomal RNA, partial sequence, strain: JCM 17835 | AB643473 | 1507 | nuccore | 168379 |
| 20218 | Halorhodospira neutrophila partial 16S rRNA gene, strain SG3301 | AJ318525 | 1356 | nuccore | 168379 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halorhodospira neutriphila DSM 15116 | GCA_016584055 | contig | ncbi | 168379 |
| 66792 | Halorhodospira neutriphila strain DSM 15116 | 168379.4 | wgs | patric | 168379 |
GC content
- @ref: 67770
- GC-content: 74.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 94 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.75 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 52.182 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.847 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 68.382 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 86.263 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 73.998 | no |
External links
@ref: 5718
culture collection no.: DSM 15116, SG 3301, JCM 17835
straininfo link
- @ref: 73779
- straininfo: 100679
literature
- topic: Phylogeny
- Pubmed-ID: 12656167
- title: Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira.
- authors: Hirschler-Rea A, Matheron R, Riffaud C, Moune S, Eatock C, Herbert RA, Willison JC, Caumette P
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02226-0
- year: 2003
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Ecosystem, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Hydrogen-Ion Concentration, Light, Mediterranean Region, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Pigments, Biological/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sodium Chloride/isolation & purification, Sulfur/metabolism
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5718 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15116) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15116 | |||
| 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) | |||
| 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. | 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) | |||
| 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 | |||
| 73779 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100679.1 | StrainInfo: A central database for resolving microbial strain identifiers |