Strain identifier

BacDive ID: 130841

Type strain: Yes

Species: Arenicella chitinivorans

Strain history: <- LMG <- O. Nedashkovskaya, Russian Academy of Sciences

NCBI tax ID(s): 1329800 (species)

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General

@ref: 22078

BacDive-ID: 130841

DSM-Number: 100248

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

description: Arenicella chitinivorans DSM 100248 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin .

NCBI tax id

  • NCBI tax id: 1329800
  • Matching level: species

strain history

  • @ref: 22078
  • history: <- LMG <- O. Nedashkovskaya, Russian Academy of Sciences

doi: 10.13145/bacdive130841.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Arenicellales
  • family: Arenicellaceae
  • genus: Arenicella
  • species: Arenicella chitinivorans
  • full scientific name: Arenicella chitinivorans Nedashkovskaya et al. 2013

@ref: 22078

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Arenicellales

family: Arenicellaceae

genus: Arenicella

species: Arenicella chitinivorans

full scientific name: Arenicella chitinivorans Nedashkovskaya et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31082negative2.7 µm0.55 µmrod-shapedno
69480negative99.997

pigmentation

  • @ref: 31082
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22078
  • 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
22078positivegrowth25mesophilic
31082positivegrowth04-38
31082positiveoptimum26.5mesophilic

culture pH

@refabilitytypepHPH range
31082positivegrowth5.5-10.5alkaliphile
31082positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 31082
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
31082NaClpositivegrowth0.5-5 %
31082NaClpositiveoptimum2.25 %

observation

  • @ref: 31082
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3108216449alanine+carbon source
3108222599arabinose+carbon source
3108222653asparagine+carbon source
3108217057cellobiose+carbon source
3108228260galactose+carbon source
3108217234glucose+carbon source
3108229987glutamate+carbon source
3108217306maltose+carbon source
3108229864mannitol+carbon source
3108237684mannose+carbon source
3108226271proline+carbon source
3108226546rhamnose+carbon source
3108217992sucrose+carbon source
3108226986threonine+carbon source
310824853esculin+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
31082acid phosphatase+3.1.3.2
31082alkaline phosphatase+3.1.3.1
31082catalase+1.11.1.6
31082gelatinase+
31082cytochrome 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
22078-----++-+----+-------

Isolation, sampling and environmental information

isolation

  • @ref: 22078
  • sample type: sea urchin (Strongylocentrotus intermedius)
  • host species: Strongylocentrotus intermedius
  • geographic location: Pacific Ocean, Sea of Japan, Troitsa Bay
  • country: Russia
  • origin.country: RUS
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_53362.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1076;96_13111;97_24205;98_30613;99_53362&stattab=map
  • Last taxonomy: Arenicella chitinivorans subclade
  • 16S sequence: KC136313
  • Sequence Identity:
  • Total samples: 538
  • soil counts: 10
  • aquatic counts: 501
  • animal counts: 23
  • plant counts: 4

Safety information

risk assessment

  • @ref: 22078
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22078
  • description: Arenicella chitinivorans strain KMM 6208 16S ribosomal RNA gene, partial sequence
  • accession: KC136313
  • length: 1488
  • database: ena
  • NCBI tax ID: 1329800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenicella chitinivorans KCTC 12711GCA_014651515scaffoldncbi1329800
66792Arenicella chitinivorans strain KCTC 127111329800.3wgspatric1329800

GC content

  • @ref: 22078
  • GC-content: 46.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno92.065yes
gram-positiveno98.846no
anaerobicno99.363yes
aerobicyes95.883no
halophileno62.614no
spore-formingno97.267no
thermophileno99.476yes
glucose-utilyes85.328yes
motileno88.407yes
glucose-fermentno91.405no

External links

@ref: 22078

culture collection no.: DSM 100248, KCTC 12711, LMG 26983, KMM 6208

straininfo link

  • @ref: 89328
  • straininfo: 282893

literature

  • topic: Phylogeny
  • Pubmed-ID: 23771619
  • title: Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius.
  • authors: Nedashkovskaya OI, Cleenwerck I, Zhukova NV, Kim SB, de Vos P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.051599-0
  • year: 2013
  • mesh: Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strongylocentrotus/*microbiology, Ubiquinone/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
22078Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100248Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100248)
31082Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172741128776041
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
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/
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
89328Reimer, 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-ID282893.1