Strain identifier

BacDive ID: 13870

Type strain: Yes

Species: Rhodobium orientis

Strain history: A. Hiraishi MB312.

NCBI tax ID(s): 34017 (species)

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General

@ref: 4281

BacDive-ID: 13870

DSM-Number: 11290

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Rhodobium orientis DSM 11290 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.

NCBI tax id

  • NCBI tax id: 34017
  • Matching level: species

strain history

@refhistory
4281<- JCM <- A. Hiraishi, MB 312
67770A. Hiraishi MB312.

doi: 10.13145/bacdive13870.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhodobiaceae
  • genus: Rhodobium
  • species: Rhodobium orientis
  • full scientific name: Rhodobium orientis Hiraishi et al. 1995

@ref: 4281

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhodobiaceae

genus: Rhodobium

species: Rhodobium orientis

full scientific name: Rhodobium orientis Hiraishi et al. 1995 emend. Urdiain et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.998

Culture and growth conditions

culture medium

  • @ref: 4281
  • name: RHODOBIUM MEDIUM (DSMZ Medium 745)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/745
  • composition: Name: RHODOBIUM MEDIUM (DSMZ Medium 745) Composition: NaCl 50.2 g/l Na-DL-malate 3.6 g/l Yeast extract 1.0 g/l KH2PO4 1.0 g/l (NH4)2SO4 1.0 g/l Na2S2O3 x 5 H2O 0.5 g/l MgCl2 x 6 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l H3BO3 6.2e-05 g/l Na2MoSO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
4281positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4281
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

observation

  • @ref: 67770
  • observation: quinones: Q-10, MK-10

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4281coastal seawaterMakurazakiJapanJPNAsia
67770Coastal seawaterMakurazakiJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_60542.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_26621;97_33425;98_42966;99_60542&stattab=map
  • Last taxonomy: Rhodobium
  • 16S sequence: D30792
  • Sequence Identity:
  • Total samples: 1047
  • soil counts: 181
  • aquatic counts: 736
  • animal counts: 81
  • plant counts: 49

Safety information

risk assessment

  • @ref: 4281
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodobium orientis strain DSM 11290 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU786783700ena34017
4281Rhodobium orientis 16S rRNA gene, complete sequenceD307921408ena34017

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodobium orientis DSM 11290GCA_014197785contigncbi34017
66792Rhodobium orientis DSM 11290GCA_016653375scaffoldncbi34017
66792Rhodobium orientis DSM 11290GCA_003258835scaffoldncbi34017
66792Rhodobium orientis strain DSM 1129034017.7wgspatric34017
66792Rhodobium orientis strain DSM 1129034017.6wgspatric34017
66792Rhodobium orientis strain DSM 1129034017.4wgspatric34017
66792Rhodobium orientis DSM 112902887616557draftimg34017
66792Rhodobium orientis DSM 112902838101865draftimg34017

GC content

  • @ref: 4281
  • GC-content: 65.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno62.704no
gram-positiveno98.517no
anaerobicno65.116yes
aerobicno65.403no
halophileno65.198no
spore-formingno95.772no
thermophileno88.537yes
glucose-utilyes90.204no
motileyes83.166no
glucose-fermentno90.332no

External links

@ref: 4281

culture collection no.: DSM 11290, JCM 9337, ATCC 51972, NCIMB 13423

straininfo link

  • @ref: 83046
  • straininfo: 43269

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473235
  • title: Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern.
  • authors: Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Imhoff JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64843-0
  • year: 2007
  • mesh: Alphaproteobacteria/chemistry/*classification/*isolation & purification/physiology, Bacteriochlorophyll A/analysis, Carbon/metabolism, Carotenoids/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Organelles/ultrastructure, Peptones/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4281Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11290)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11290
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83046Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43269.1StrainInfo: A central database for resolving microbial strain identifiers