Strain identifier

BacDive ID: 14049

Type strain: Yes

Species: Lewinella agarilytica

Strain Designation: SST-19

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 478744 (species)

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General

@ref: 17747

BacDive-ID: 14049

DSM-Number: 24740

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

description: Lewinella agarilytica SST-19 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from beach sediment.

NCBI tax id

  • NCBI tax id: 478744
  • Matching level: species

strain history

@refhistory
17747<- KCTC <- S. D. Lee, Jeju National Univ., Rep. of Korea
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive14049.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Saprospiria
  • order: Saprospirales
  • family: Lewinellaceae
  • genus: Lewinella
  • species: Lewinella agarilytica
  • full scientific name: Lewinella agarilytica Lee 2007

  • synonyms

    • @ref: 20215
    • synonym: Neolewinella agarilytica

@ref: 17747

domain: Bacteria

phylum: Bacteroidetes

class: Saprospiria

order: Sphingobacteriales

family: Lewinellaceae

genus: Lewinella

species: Lewinella agarilytica

full scientific name: Lewinella agarilytica Lee 2007

strain designation: SST-19

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32283negative3.25 µm0.5 µmrod-shapedyesgliding
67771rod-shapedgliding
67771filament-shaped
67771negative
69480negative99.993

pigmentation

  • @ref: 32283
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17747
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
17747positivegrowth28mesophilic
32283positivegrowth04-37
32283positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32283positivegrowth5.1-10.1alkaliphile
32283positiveoptimum8.6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32283aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.934

halophily

  • @ref: 32283
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3228316947citrate+carbon source
322835417glucosamine+carbon source
3228317234glucose+carbon source
3228325115malate+carbon source
3228317306maltose+carbon source
3228337684mannose+carbon source
322834853esculin+hydrolysis

enzymes

@refvalueactivityec
32283acid phosphatase+3.1.3.2
32283alkaline phosphatase+3.1.3.1
32283catalase+1.11.1.6
32283gelatinase+
32283cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17747beach sedimentJejuRepublic of KoreaKORAsia
67771From beach sedimentJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_26286.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_489;96_13129;97_15946;98_19744;99_26286&stattab=map
  • Last taxonomy: Lewinella agarilytica subclade
  • 16S sequence: AM286229
  • Sequence Identity:
  • Total samples: 279
  • soil counts: 13
  • aquatic counts: 255
  • animal counts: 9
  • plant counts: 2

Safety information

risk assessment

  • @ref: 17747
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17747
  • description: Lewinella agarilytica partial 16S rRNA gene, type strain SST-19T
  • accession: AM286229
  • length: 1415
  • database: ena
  • NCBI tax ID: 478744

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neolewinella agarilytica DSM 24740GCA_900110645scaffoldncbi478744
66792Lewinella agarilytica strain DSM 24740478744.3wgspatric478744
66792Lewinella agarilytica DSM 247402693429910draftimg478744

GC content

  • @ref: 67771
  • GC-content: 51.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno87.446no
motileno91.649no
flagellatedno96.942no
gram-positiveno96.969yes
anaerobicno99.17no
aerobicyes78.702no
halophileno73.527no
spore-formingno94.995no
thermophileno95.045no
glucose-utilyes86.38yes

External links

@ref: 17747

culture collection no.: DSM 24740, JBRI 2009, JCM 14216, KCTC 12774

straininfo link

  • @ref: 83218
  • straininfo: 323257

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048730Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65254-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny28875904Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments.Kang H, Kim H, Joung Y, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0021762017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33054906Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater.Kim I, Chhetri G, Kim J, Kang M, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0045152020Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, Carotenoids/*chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17747Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24740)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24740
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
32283Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2852328776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83218Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323257.1StrainInfo: A central database for resolving microbial strain identifiers