Strain identifier

BacDive ID: 134138

Type strain: Yes

Species: Roseivirga echinicomitans

Strain history: <- KCTC 12370

NCBI tax ID(s): 296218 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 66352

BacDive-ID: 134138

DSM-Number: 102948

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

description: Roseivirga echinicomitans KCTC 12370 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from sea urchin.

NCBI tax id

  • NCBI tax id: 296218
  • Matching level: species

strain history

  • @ref: 66352
  • history: <- KCTC 12370

doi: 10.13145/bacdive134138.20230509.8.1

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 echinicomitans
  • full scientific name: Roseivirga echinicomitans Nedashkovskaya et al. 2005

@ref: 66352

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Roseivirgaceae

genus: Roseivirga

species: Roseivirga echinicomitans

full scientific name: Roseivirga echinicomitans Nedashkovskaya et al. 2005 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31464negative2.65 µm0.4 µmrod-shapedno
69480negative99.987

pigmentation

  • @ref: 31464
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 66352
  • 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
31464positivegrowth04-31
31464positiveoptimum22psychrophilic
66352positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31464
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31464no
69481no100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
31464NaClpositivegrowth01-08 %
31464NaClpositiveoptimum4 %

observation

  • @ref: 31464
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31464620642,3-butanediol+carbon source
3146416947citrate+carbon source
3146428260galactose+carbon source
3146424175galacturonate+carbon source
3146417754glycerol+carbon source
3146417596inosine+carbon source
3146425017leucine+carbon source
3146417306maltose+carbon source
31464506227N-acetylglucosamine+carbon source
3146418257ornithine+carbon source
3146428044phenylalanine+carbon source
3146426271proline+carbon source
3146430911sorbitol+carbon source
3146417748thymidine+carbon source
314644853esculin+hydrolysis
3146417632nitrate+reduction

enzymes

  • @ref: 31464
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

  • @ref: 31464
  • sample type: sea urchin

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_4834.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_492;96_2388;97_2904;98_3620;99_4834&stattab=map
  • Last taxonomy: Roseivirga
  • 16S sequence: AY753206
  • Sequence Identity:
  • Total samples: 1110
  • soil counts: 42
  • aquatic counts: 992
  • animal counts: 68
  • plant counts: 8

Safety information

risk assessment

  • @ref: 66352
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 31464
  • description: Roseivirga echinicomitans strain KMM 6058 16S ribosomal RNA gene, partial sequence
  • accession: AY753206
  • length: 1415
  • database: nuccore
  • NCBI tax ID: 296218

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseivirga echinicomitans KMM 6058GCA_001592935contigncbi296218
66792Roseivirga echinicomitans strain KMM 6058296218.3wgspatric296218
66792Roseivirga echinicomitans KMM 60582651870325draftimg296218

GC content

@refGC-contentmethod
3146441.3
6635240.0sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.447no
anaerobicno99.389no
halophileno82.588no
spore-formingno96.306no
glucose-utilyes84.372no
flagellatedno98.181yes
thermophileno97.672yes
aerobicyes93.413yes
motileno93.398yes
glucose-fermentno91.589no

External links

@ref: 66352

culture collection no.: KCTC 12370, LMG 22587, KMM 6058, DSM 102948

straininfo link

  • @ref: 91737
  • straininfo: 133050

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166668
  • title: Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga.
  • authors: Nedashkovskaya OI, Kim SB, Lysenko AM, Park MS, Mikhailov VV, Bae KS, Park HY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63621-0
  • year: 2005
  • mesh: Animals, Base Composition, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Strongylocentrotus/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31464Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172776528776041
66352Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102948Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102948)
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
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91737Reimer, 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-ID133050.1