Strain identifier

BacDive ID: 5485

Type strain: Yes

Species: Arenibacter echinorum

Strain history: <- KCTC; KCTC 22013 <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia

NCBI tax ID(s): 440515 (species)

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General

@ref: 17258

BacDive-ID: 5485

DSM-Number: 23522

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

description: Arenibacter echinorum DSM 23522 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin Strongylocentrotus intermedius.

NCBI tax id

  • NCBI tax id: 440515
  • Matching level: species

strain history

  • @ref: 17258
  • history: <- KCTC; KCTC 22013 <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia

doi: 10.13145/bacdive5485.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Arenibacter
  • species: Arenibacter echinorum
  • full scientific name: Arenibacter echinorum Nedashkovskaya et al. 2007

@ref: 17258

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Arenibacter

species: Arenibacter echinorum

full scientific name: Arenibacter echinorum Nedashkovskaya et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32280negative2.1 µm0.45 µmrod-shapedyesgliding
69480negative99.981

pigmentation

  • @ref: 32280
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17258
  • 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
17258positivegrowth28mesophilic
32280positivegrowth04-35
32280positiveoptimum25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 32280
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32280NaClpositivegrowth0-8 %
32280NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3228022599arabinose+carbon source
3228017057cellobiose+carbon source
3228016947citrate+carbon source
3228023652dextrin+carbon source
3228017234glucose+carbon source
3228024996lactate+carbon source
3228017716lactose+carbon source
3228025115malate+carbon source
3228017306maltose+carbon source
3228029864mannitol+carbon source
3228037684mannose+carbon source
3228028053melibiose+carbon source
3228051850methyl pyruvate+carbon source
3228016634raffinose+carbon source
3228026546rhamnose+carbon source
3228017992sucrose+carbon source
3228027082trehalose+carbon source
3228018222xylose+carbon source

enzymes

@refvalueactivityec
32280acid phosphatase+3.1.3.2
32280alkaline phosphatase+3.1.3.1
32280alpha-galactosidase+3.2.1.22
32280catalase+1.11.1.6
32280cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 17258
  • sample type: sea urchin Strongylocentrotus intermedius
  • host species: Strongylocentrotus intermedius
  • geographic location: Troitsa Bay, Gulf of Peter the Great, Sea of Japan
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Echinodermata
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2346.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_1267;97_1502;98_1829;99_2346&stattab=map
  • Last taxonomy: Arenibacter
  • 16S sequence: EF536748
  • Sequence Identity:
  • Total samples: 9391
  • soil counts: 1235
  • aquatic counts: 7063
  • animal counts: 925
  • plant counts: 168

Safety information

risk assessment

  • @ref: 17258
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17258
  • description: Arenibacter echinorum strain KMM 6032 16S ribosomal RNA gene, partial sequence
  • accession: EF536748
  • length: 1431
  • database: ena
  • NCBI tax ID: 440515

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenibacter echinorum DSM 23522GCA_003259375scaffoldncbi440515
66792Arenibacter echinorum strain DSM 23522440515.3wgspatric440515
66792Arenibacter echinorum DSM 235222593339296draftimg440515

GC content

@refGC-content
1725839-40
3228039.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.736no
flagellatedno94.537no
gram-positiveno97.826yes
anaerobicno99.649no
aerobicyes91.581yes
halophileno86.078yes
spore-formingno96.092no
glucose-utilyes90.79yes
thermophileno99.252yes
glucose-fermentno88.31no

External links

@ref: 17258

culture collection no.: DSM 23522, KCTC 22013, LMG 22574, KMM 6032

straininfo link

  • @ref: 74972
  • straininfo: 132526

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978235Arenibacter echinorum sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.Nedashkovskaya OI, Kim SB, Lysenko AM, Lee KH, Bae KS, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.65251-02007Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Strongylocentrotus/*microbiologyGenetics
Phylogeny22544794Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat.Jeong SH, Jin HM, Kim JM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.040683-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17258Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23522)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23522
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
32280Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2852028776041
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)
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
74972Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132526.1StrainInfo: A central database for resolving microbial strain identifiers