Strain identifier
BacDive ID: 132270
Type strain: 
Species: Spiribacter vilamensis
Strain Designation: SV525
Strain history: R. J. Menes; Univ. de la República, Uruguay; SV525.
NCBI tax ID(s): 531306 (species)
version 9.3 (current version)
General
@ref: 24059
BacDive-ID: 132270
DSM-Number: 21056
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Spiribacter vilamensis SV525 is a mesophilic, Gram-negative bacterium that was isolated from sediment from a hypersaline lagoon.
NCBI tax id
- NCBI tax id: 531306
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24059 | <- J. Menes, Facultad Quimica, Montevideo, Uruguay; SV525 |
| 67770 | R. J. Menes; Univ. de la República, Uruguay; SV525. |
doi: 10.13145/bacdive132270.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Ectothiorhodospiraceae
- genus: Spiribacter
- species: Spiribacter vilamensis
- full scientific name: Spiribacter vilamensis (Menes et al. 2016) León et al. 2020
synonyms
- @ref: 20215
- synonym: Halopeptonella vilamensis
@ref: 24059
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Spiribacter
species: Spiribacter vilamensis
full scientific name: Spiribacter vilamensis Leon et al. 2020
strain designation: SV525
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 99.2 |
| 125438 | negative | 97.5 |
Culture and growth conditions
culture medium
- @ref: 24059
- name: MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514b
- composition: Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b; with strain-specific modifications) Composition: NaCl 60.0 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 24059 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 98.8 |
| 125438 | no | 92.852 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24059 | sediment from a hypersaline lagoon | Jujuy, Laguna Vilama (22° 35' S 66° 55' W at 4600 m above sea level) | Argentina | ARG | Middle and South America | -22.5833 | -66.9168 |
| 67770 | Sediment from a hypersaline lake located at 4,600 m above sea level | Laguna Vilama | Argentina | ARG | Middle and South America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_44799.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15363;96_653;97_3122;98_3921;99_44799&stattab=map
- Last taxonomy: Spiribacter
- 16S sequence: EU557314
- Sequence Identity:
- Total samples: 17
- soil counts: 3
- aquatic counts: 14
Safety information
risk assessment
- @ref: 24059
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24059
- description: Spiribacter vilamensis strain SV525 16S ribosomal RNA gene, partial sequence
- accession: EU557314
- length: 1437
- database: nuccore
- NCBI tax ID: 531306
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Spiribacter vilamensis DSM 21056 | GCA_007625165 | scaffold | ncbi | 531306 |
| 66792 | Halopeptonella vilamensis strain DSM 21056 | 531306.4 | wgs | patric | 531306 |
| 66792 | Halopeptonella vilamensis strain DSM 21056 | 531306.3 | wgs | patric | 531306 |
| 66792 | Halopeptonella vilamensis DSM 21056 | 2802429687 | draft | img | 531306 |
| 67770 | Spiribacter vilamensis DSM 21056 | GCA_004217415 | contig | ncbi | 531306 |
GC content
- @ref: 24059
- GC-content: 60.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 85.379 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 60.558 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.852 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 92.677 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 73.634 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 81.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 81.5 |
External links
@ref: 24059
culture collection no.: DSM 21056, JCM 16388, NCIMB 14596
straininfo link
- @ref: 90617
- straininfo: 405587
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26475627 | Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae. | Menes RJ, Viera CE, Farias ME, Seufferheld MJ | Extremophiles | 10.1007/s00792-015-0793-7 | 2016 | Bacterial Proteins/genetics/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, Ectothiorhodospiraceae/classification/genetics/*isolation & purification/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
| Phylogeny | 32238225 | Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov. | Leon MJ, Galisteo C, Ventosa A, Sanchez-Porro C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004113 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Ectothiorhodospiraceae/*classification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 24059 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21056 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21056) | |
| 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/ | |
| 90617 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID405587.1 | |
| 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 |