Strain identifier

BacDive ID: 131264

Type strain: Yes

Species: Roseivirga pacifica

Strain Designation: DY53

Strain history: X.-W. Xu DY53.

NCBI tax ID(s): 1267423 (species)

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General

@ref: 22491

BacDive-ID: 131264

DSM-Number: 100771

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Roseivirga pacifica DY53 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater from 2672 m depth.

NCBI tax id

  • NCBI tax id: 1267423
  • Matching level: species

strain history

@refhistory
22491<- JCM <- X. W. Xu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; DY53
67770X.-W. Xu DY53.

doi: 10.13145/bacdive131264.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Roseivirgaceae
  • genus: Roseivirga
  • species: Roseivirga pacifica
  • full scientific name: Roseivirga pacifica (Huo et al. 2013) García-López et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Fabibacter pacificus

@ref: 22491

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Roseivirgaceae

genus: Roseivirga

species: Roseivirga pacifica

full scientific name: Roseivirga pacifica (Huo et al. 2013) García-López et al. 2020

strain designation: DY53

type strain: yes

Morphology

cell morphology

  • @ref: 31070
  • gram stain: negative
  • cell length: 3.25 µm
  • cell width: 0.6 µm
  • cell shape: rod-shaped

pigmentation

  • @ref: 31070
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22491
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22491positivegrowth37mesophilic
31070positivegrowth15-40
31070positiveoptimum36mesophilic
67770positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
31070positivegrowth6.5-8.5alkaliphile
31070positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31070
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
31070NaClpositivegrowth0.5-15 %
31070NaClpositiveoptimum2 %

observation

@refobservation
31070aggregates in clumps
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3107016449alanine+carbon source
3107029016arginine+carbon source
3107035391aspartate+carbon source
3107017057cellobiose+carbon source
3107028757fructose+carbon source
3107028260galactose+carbon source
3107024265gluconate+carbon source
3107017234glucose+carbon source
3107029987glutamate+carbon source
3107017754glycerol+carbon source
3107027570histidine+carbon source
3107017716lactose+carbon source
3107017306maltose+carbon source
3107037684mannose+carbon source
3107018257ornithine+carbon source
3107015361pyruvate+carbon source
3107016634raffinose+carbon source
3107017814salicin+carbon source
3107030031succinate+carbon source
3107017992sucrose+carbon source
3107027082trehalose+carbon source
310704853esculin+hydrolysis
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
31070acid phosphatase+3.1.3.2
31070alkaline phosphatase+3.1.3.1
31070catalase+1.11.1.6
31070cytochrome oxidase+1.9.3.1
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22491-----+-+-----+------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
22491seawater from 2672 m depthEast5.3004106.487
67770Deep-seawater sample from the eastern Pacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_91054.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_492;96_2755;97_47879;98_62771;99_91054&stattab=map
  • Last taxonomy: Roseivirga pacifica subclade
  • 16S sequence: KC005305
  • Sequence Identity:
  • Total samples: 472
  • soil counts: 5
  • aquatic counts: 448
  • animal counts: 16
  • plant counts: 3

Safety information

risk assessment

  • @ref: 22491
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22491
  • description: Fabibacter pacificus strain DY53 16S ribosomal RNA gene, partial sequence
  • accession: KC005305
  • length: 1442
  • database: ena
  • NCBI tax ID: 1267423

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fabibacter pacificus strain CGMCC 1.124021267423.4wgspatric1267423
66792Fabibacter pacificus strain DSM 1007711267423.11wgspatric1267423
66792Fabibacter pacificus DSM 1007712728369263draftimg1267423
66792Fabibacter pacificus CGMCC 1.124022667527390draftimg1267423
67770Roseivirga pacifica CGMCC 1.12402GCA_900111145contigncbi1267423
67770Roseivirga pacifica DSM 100771GCA_003633845scaffoldncbi1267423

GC content

@refGC-contentmethod
3107040.8
2249140.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.508no
gram-positiveno97.654yes
anaerobicno99.112no
aerobicyes92.488yes
halophileno85.864no
spore-formingno95.719no
glucose-utilyes88.609no
flagellatedno97.354no
thermophileno97.715yes
glucose-fermentno91.382yes

External links

@ref: 22491

culture collection no.: DSM 100771, CGMCC 1.12402, JCM 18885

straininfo link

  • @ref: 89708
  • straininfo: 398197

literature

  • topic: Phylogeny
  • Pubmed-ID: 23625263
  • title: Fabibacter pacificus sp. nov., a moderately halophilic bacterium isolated from seawater.
  • authors: Huo YY, Xu L, Wang CS, Yang JY, You H, Oren A, Xu XW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.051276-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22491Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100771Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100771)
31070Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172739928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89708Reimer, 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 identifiers10.60712/SI-ID398197.1