Strain identifier
BacDive ID: 11902
Type strain:
Species: Hydrogenovibrio marinus
Strain history: T. Kodama MH-110.
NCBI tax ID(s): 1123513 (strain), 28885 (species)
version 8.1 (current version)
General
@ref: 4273
BacDive-ID: 11902
DSM-Number: 11271
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Hydrogenovibrio marinus DSM 11271 is a mesophilic bacterium that was isolated from sea water.
NCBI tax id
NCBI tax id | Matching level |
---|---|
28885 | species |
1123513 | strain |
strain history
@ref | history |
---|---|
4273 | <- JCM <- T. Kodama, strain MH-110 |
67770 | T. Kodama MH-110. |
doi: 10.13145/bacdive11902.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Hydrogenovibrio
- species: Hydrogenovibrio marinus
- full scientific name: Hydrogenovibrio marinus Nishihara et al. 1991
@ref: 4273
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Hydrogenovibrio
species: Hydrogenovibrio marinus
full scientific name: Hydrogenovibrio marinus Nishihara et al. 1991
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4273 | MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) | yes | https://mediadive.dsmz.de/medium/81 | Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l Nicotinic acid 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Calcium pantothenate 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water |
4273 | HYDROGENOBACTER HALOPHILUS MEDIUM (DSMZ Medium 744) | yes | https://mediadive.dsmz.de/medium/744 | Name: HYDROGENOBACTER HALOPHILUS MEDIUM (DSMZ Medium 744) Composition: NaCl 29.3 g/l K2HPO4 2.5 g/l (NH4)2SO4 2.0 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 0.01 g/l FeSO4 x 7 H2O 0.01 g/l ZnSO4 x 7 H2O 1.4e-05 g/l CoCl2 x 6 H2O 2e-06 g/l MnSO4 x 5 H2O 2e-06 g/l MoO3 2e-06 g/l H3BO3 2e-06 g/l CuSO4 x 5 H2O 1e-06 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4273 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
compound production
- @ref: 4273
- compound: ribulose-1,5-bisphosphate carboxylase
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4273 | sea water | Shonan Coast, Kanagawa | Japan | JPN | Asia |
67770 | Seawater of the Shonan Coast | Kanagawa Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_3577.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_118;96_1109;97_2235;98_2741;99_3577&stattab=map
- Last taxonomy: Hydrogenovibrio marinus subclade
- 16S sequence: D86374
- Sequence Identity:
- Total samples: 753
- soil counts: 84
- aquatic counts: 542
- animal counts: 113
- plant counts: 14
Safety information
risk assessment
- @ref: 4273
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Hydrogenovibrio marinus gene for 16S rRNA, partial sequence
- accession: D86374
- length: 1409
- database: ena
- NCBI tax ID: 28885
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Hydrogenovibrio marinus DSM 11271 | 1123513.6 | wgs | patric | 1123513 |
66792 | Hydrogenovibrio marinus strain MH-110 | 28885.6 | complete | patric | 28885 |
66792 | Hydrogenovibrio marinus DSM 11271 | 2571042915 | draft | img | 1123513 |
67770 | Hydrogenovibrio marinus MH-110 | GCA_000696325 | scaffold | ncbi | 28885 |
67770 | Hydrogenovibrio marinus DSM 11271 | GCA_000711315 | contig | ncbi | 1123513 |
GC content
@ref | GC-content | method |
---|---|---|
4273 | 44.1 | |
67770 | 44.1 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 99.003 | no |
anaerobic | no | 94.753 | no |
halophile | no | 76.264 | no |
spore-forming | no | 95.882 | no |
glucose-util | yes | 59.364 | no |
motile | yes | 91.841 | no |
flagellated | yes | 85.299 | no |
aerobic | no | 87.406 | no |
thermophile | no | 94.899 | yes |
glucose-ferment | no | 86.344 | no |
External links
@ref: 4273
culture collection no.: DSM 11271, JCM 7688
straininfo link
- @ref: 81117
- straininfo: 49062
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4273 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11271) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11271 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
81117 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49062.1 | StrainInfo: A central database for resolving microbial strain identifiers |