Strain identifier
BacDive ID: 162622
Type strain: 
Species: Hydrogenimonas urashimensis
Strain Designation: SSM-sur55
Strain history: <- S. Mino, Univ. Hokkaido, Japan; SSM-sur55 {2020} <- S. Taiki, Graduate School of Fisheries Sciences, Hokkaido University, Japan;
NCBI tax ID(s): 2740515 (species)
version 9.1 (current version)
General
@ref: 67770
BacDive-ID: 162622
DSM-Number: 111344
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Hydrogenimonas urashimensis SSM-sur55 is a Gram-negative bacterium that was isolated from Chimny structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean.
NCBI tax id
- NCBI tax id: 2740515
- Matching level: species
strain history
| @ref | history |
|---|---|
| 67770 | S. Mino SSM-sur55. |
| 69105 | <- S. Mino, Univ. Hokkaido, Japan; SSM-sur55 {2020} <- S. Taiki, Graduate School of Fisheries Sciences, Hokkaido University, Japan; |
doi: 10.13145/bacdive162622.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Hydrogenimonadaceae
- genus: Hydrogenimonas
- species: Hydrogenimonas urashimensis
- full scientific name: Hydrogenimonas urashimensis Mino et al. 2021
@ref: 67770
domain: Bacteria
phylum: Pseudomonadota
class: Epsilonproteobacteria
order: Campylobacterales
family: Hydrogenimonadaceae
genus: Hydrogenimonas
species: Hydrogenimonas urashimensis
full scientific name: Hydrogenimonas urashimensis Mino et al. 2021
strain designation: SSM-sur55
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.383
multimedia
- @ref: 69105
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_111344.jpg
- caption: DSM 111344; scale bar small represents 1 µm, scale bar big represents 5 µm
- intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Culture and growth conditions
culture medium
- @ref: 69105
- name: MMJHS MEDIUM (DSMZ Medium 1721)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1721.pdf
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 67770 | positive | growth | 55 |
| 69105 | positive | growth | 55 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 93.69 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 67770 | Chimny structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean | ||||||
| 69105 | Baltan chimney at Urashima site in the South Mariana Trough | Deep-sea hydrothermal vent in the South Mariana Trough | USA | USA | North America | 12.9167 | 143.667 |
Sequence information
16S sequences
- @ref: 67770
- description: Hydrogenimonas sp. SSM-sur55 gene for 16S ribosomal RNA, partial sequence
- accession: LC469141
- length: 1536
- database: nuccore
- NCBI tax ID: 2231112
Genome sequences
- @ref: 67770
- description: Hydrogenimonas urashimensis SSM-sur55
- accession: GCA_016593255
- assembly level: complete
- database: ncbi
- NCBI tax ID: 2740515
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 52.8 | genome sequence analysis |
| 69105 | 52.8 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.383 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 54.4 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 80.084 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.69 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 50.752 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 65.17 | no |
External links
@ref: 67770
culture collection no.: JCM 19825, KCTC 15926, DSM 111344
straininfo link
- @ref: 113509
- straininfo: 399442
literature
- topic: Phylogeny
- Pubmed-ID: 33340909
- title: Hydrogenimonas urashimensis sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the Southern Mariana Trough.
- authors: Mino S, Shiotani T, Nakagawa S, Takai K, Sawabe T
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2020.126170
- year: 2020
- mesh: Ammonium Compounds, Carbon Dioxide, Epsilonproteobacteria/*classification/isolation & purification, Hydrogen, Hydrothermal Vents/*microbiology, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfur
- topic2: Enzymology
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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69105 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-111344 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 111344) | |
| 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 | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 113509 | 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-ID399442.1 |