Strain identifier

BacDive ID: 13768

Type strain: Yes

Species: Roseovarius nubinhibens

Strain Designation: ISM

Strain history: <- M. A. Moran; ISM <- J. M. González <- J. A. Fuhrman <- J. S. Covert <- S. H. Lee

NCBI tax ID(s): 314263 (species)

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General

@ref: 5736

BacDive-ID: 13768

DSM-Number: 15170

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Roseovarius nubinhibens ISM is a mesophilic bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 314263
  • Matching level: species

strain history

  • @ref: 5736
  • history: <- M. A. Moran; ISM <- J. M. González <- J. A. Fuhrman <- J. S. Covert <- S. H. Lee

doi: 10.13145/bacdive13768.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseovarius
  • species: Roseovarius nubinhibens
  • full scientific name: Roseovarius nubinhibens González et al. 2003

@ref: 5736

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseovarius

species: Roseovarius nubinhibens

full scientific name: Roseovarius nubinhibens González et al. 2003

strain designation: ISM

type strain: yes

Morphology

colony morphology

  • @ref: 5736
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 5736
  • name: 1/2 YTSS MEDIUM (DSMZ Medium 974)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/974
  • composition: Name: 1/2 YTSS MEDIUM (DSMZ Medium 974) Composition: Sea Salt 20.0 g/l Agar 15.0 g/l Yeast extract 2.0 g/l Tryptone 1.25 g/l Distilled water

culture temp

  • @ref: 5736
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
5736catalase+1.11.1.6
5736cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
5736--------------------

Isolation, sampling and environmental information

isolation

  • @ref: 5736
  • sample type: seawater
  • geographic location: Caribbean Sea

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5075.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2275;97_3020;98_3788;99_5075&stattab=map
  • Last taxonomy: Roseovarius nubinhibens subclade
  • 16S sequence: AF098495
  • Sequence Identity:
  • Total samples: 886
  • soil counts: 23
  • aquatic counts: 796
  • animal counts: 67

Safety information

risk assessment

  • @ref: 5736
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseovarius nubinhibens strain DSM15170 16S ribosomal RNA gene, partial sequenceDQ9156251309ena314263
5736Roseobacter sp. ISM 16S ribosomal RNA gene, partial sequenceAF0984951418ena89187

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseovarius nubinhibens ISMGCA_000152625scaffoldncbi89187
66792Roseovarius nubinhibens ISM89187.6wgspatric89187
66792Roseovarius nubinhibens ISM638341183draftimg89187

GC content

  • @ref: 5736
  • GC-content: 66.0±02

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno82.988no
flagellatedno94.974no
gram-positiveno98.294no
anaerobicno95.66no
aerobicyes86.391no
halophileyes74.699no
spore-formingno96.107no
thermophileno97.331yes
glucose-utilno65.06yes
glucose-fermentno93.479yes

External links

@ref: 5736

culture collection no.: DSM 15170, ATCC BAA 591

straininfo link

  • @ref: 82947
  • straininfo: 113583

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130004Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments.Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MAInt J Syst Evol Microbiol10.1099/ijs.0.02491-02003Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/isolation & purification/*metabolism, Seawater/microbiology, Species Specificity, Sulfonium Compounds/*metabolism, Sulfur/metabolismMetabolism
Phylogeny18450713Roseovarius aestuarii sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65657-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5736Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15170)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15170
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)
68369Automatically annotated from API 20NE
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
82947Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113583.1StrainInfo: A central database for resolving microbial strain identifiers