Strain identifier

BacDive ID: 11902

Type strain: Yes

Species: Hydrogenovibrio marinus

Strain history: T. Kodama MH-110.

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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 idMatching level
28885species
1123513strain

strain history

@refhistory
4273<- JCM <- T. Kodama, strain MH-110
67770T. 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

@refnamegrowthlinkcomposition
4273MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: 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
4273HYDROGENOBACTER HALOPHILUS MEDIUM (DSMZ Medium 744)yeshttps://mediadive.dsmz.de/medium/744Name: 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

@refgrowthtypetemperaturerange
4273positivegrowth37mesophilic
67770positivegrowth37mesophilic

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

@refsample typegeographic locationcountryorigin.countrycontinent
4273sea waterShonan Coast, KanagawaJapanJPNAsia
67770Seawater of the Shonan CoastKanagawa Pref.JapanJPNAsia

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrogenovibrio marinus DSM 112711123513.6wgspatric1123513
66792Hydrogenovibrio marinus strain MH-11028885.6completepatric28885
66792Hydrogenovibrio marinus DSM 112712571042915draftimg1123513
67770Hydrogenovibrio marinus MH-110GCA_000696325scaffoldncbi28885
67770Hydrogenovibrio marinus DSM 11271GCA_000711315contigncbi1123513

GC content

@refGC-contentmethod
427344.1
6777044.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno99.003no
anaerobicno94.753no
halophileno76.264no
spore-formingno95.882no
glucose-utilyes59.364no
motileyes91.841no
flagellatedyes85.299no
aerobicno87.406no
thermophileno94.899yes
glucose-fermentno86.344no

External links

@ref: 4273

culture collection no.: DSM 11271, JCM 7688

straininfo link

  • @ref: 81117
  • straininfo: 49062

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4273Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11271)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11271
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
81117Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49062.1StrainInfo: A central database for resolving microbial strain identifiers