Strain identifier
BacDive ID: 161262
Type strain: 
Species: Sulfurihydrogenibium yellowstonense
Strain history: S. Nakagawa SS-5.
NCBI tax ID(s): 304736 (species)
version 9.1 (current version)
General
@ref: 67770
BacDive-ID: 161262
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Sulfurihydrogenibium yellowstonense JCM 12773 is a Gram-negative bacterium that was isolated from Calcite Hot Spring in Yellowstone National Park.
NCBI tax id
- NCBI tax id: 304736
- Matching level: species
strain history
- @ref: 67770
- history: S. Nakagawa SS-5.
doi: 10.13145/bacdive161262.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/aquificota
- domain: Bacteria
- phylum: Aquificota
- class: Aquificia
- order: Aquificales
- family: Hydrogenothermaceae
- genus: Sulfurihydrogenibium
- species: Sulfurihydrogenibium yellowstonense
- full scientific name: Sulfurihydrogenibium yellowstonense Nakagawa et al. 2005
@ref: 67770
domain: Bacteria
phylum: Aquificae
class: Aquificae
order: Aquificales
family: Hydrogenothermaceae
genus: Sulfurihydrogenibium
species: Sulfurihydrogenibium yellowstonense
full scientific name: Sulfurihydrogenibium yellowstonense Nakagawa et al. 2005
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 94.876
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 70
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 93.331
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Calcite Hot Spring in Yellowstone National Park
- geographic location: WY
- country: USA
- origin.country: USA
- continent: North America
taxonmaps
- @ref: 69479
- File name: preview.99_31093.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_83;96_198;97_215;98_242;99_31093&stattab=map
- Last taxonomy: Sulfurihydrogenibium
- 16S sequence: AY686713
- Sequence Identity:
- Total samples: 11
- aquatic counts: 11
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Sulfurihydrogenibium yellowstonense strain SS-5 16S ribosomal RNA gene, partial sequence | AY686713 | 1447 | nuccore | 432331 |
| 124043 | Sulfurihydrogenibium yellowstonense 16S-23S rRNA intergenic spacer containing tRNA-Ile and tRNA-Ala genes, type strain JCM 12773T | AM259516 | 456 | nuccore | 432331 |
Genome sequences
- @ref: 67770
- description: Sulfurihydrogenibium yellowstonense SS-5
- accession: GCA_000173615
- assembly level: contig
- database: ncbi
- NCBI tax ID: 432331
GC content
- @ref: 67770
- GC-content: 32
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 94.876 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 57.291 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 80.035 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.331 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | yes | 75.348 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 52.432 | no |
External links
@ref: 67770
culture collection no.: JCM 12773, OCM 840
straininfo link
- @ref: 113322
- straininfo: 281467
literature
- topic: Phylogeny
- Pubmed-ID: 16280480
- title: Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense.
- authors: Nakagawa S, Shtaih Z, Banta A, Beveridge TJ, Sako Y, Reysenbach AL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63708-0
- year: 2005
- mesh: Base Composition, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Gram-Negative Chemolithotrophic Bacteria/*classification/isolation & purification/metabolism/ultrastructure, Hot Springs/*microbiology, Hot Temperature, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Sulfur Compounds/*metabolism, Temperature, *Water Microbiology, Wyoming
- topic2: Enzymology
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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/ |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 113322 | 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-ID281467.1 |
| 124043 | Dr. Isabel Schober, Dr. Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy |