Strain identifier

BacDive ID: 131475

Type strain: Yes

Species: Lewinella xylanilytica

Strain Designation: 13-9-B8

Strain history: <- Kee-Sun Shin, KRIBB

NCBI tax ID(s): 1514080 (species)

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

@ref: 22702

BacDive-ID: 131475

DSM-Number: 29526

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

description: Lewinella xylanilytica 13-9-B8 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from coastal seawater.

NCBI tax id

  • NCBI tax id: 1514080
  • Matching level: species

strain history

@refhistory
22702<- H.-R. Sung, KRIBB; 13-9-B8
67771<- Kee-Sun Shin, KRIBB

doi: 10.13145/bacdive131475.20230509.8.1

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 xylanilytica
  • full scientific name: Lewinella xylanilytica Sung et al. 2015
  • synonyms

    • @ref: 20215
    • synonym: Neolewinella xylanilytica

@ref: 22702

domain: Bacteria

phylum: Bacteroidetes

class: Saprospiria

order: Sphingobacteriales

family: Lewinellaceae

genus: Lewinella

species: Lewinella xylanilytica

full scientific name: Lewinella xylanilytica Sung et al. 2015

strain designation: 13-9-B8

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771negative
69480no94.65
69480negative99.998

Culture and growth conditions

culture medium

  • @ref: 22702
  • 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
22702positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.988

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
22702+--------+----------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22702coastal seawaterMarado, Jeju IslandRepublic of KoreaKORAsia
67771From SeawaterJeju IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_41933.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_489;96_19415;97_24096;98_30481;99_41933&stattab=map
  • Last taxonomy: Lewinella xylanilytica subclade
  • 16S sequence: KJ573521
  • Sequence Identity:
  • Total samples: 313
  • soil counts: 53
  • aquatic counts: 192
  • animal counts: 57
  • plant counts: 11

Safety information

risk assessment

  • @ref: 22702
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22702
  • description: Lewinella xylanilytica strain 13-9-B8 16S ribosomal RNA gene, partial sequence
  • accession: KJ573521
  • length: 1462
  • database: ena
  • NCBI tax ID: 1514080

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neolewinella xylanilytica DSM 29526GCA_002934605scaffoldncbi1514080
66792Lewinella xylanilytica strain DSM 295261514080.3wgspatric1514080
66792Lewinella xylanilytica DSM 295262734482073draftimg1514080

GC content

@refGC-contentmethod
2270259.1high performance liquid chromatography (HPLC)
6777159.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.158yes
gram-positiveno96.925yes
anaerobicno99.306yes
aerobicyes89.847no
halophileno76.619no
spore-formingno94.115no
glucose-utilyes88.147no
thermophileno98.819yes
motileno88.692yes
glucose-fermentno88.257yes

External links

@ref: 22702

culture collection no.: DSM 29526, KCTC 32663

straininfo link

  • @ref: 89892
  • straininfo: 402767

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26297220Lewinella xylanilytica sp. nov., a member of the family Saprospiraceae isolated from coastal seawater.Sung HR, Lee JM, Kim M, Shin KSInt J Syst Evol Microbiol10.1099/ijsem.0.0004352015Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
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

Reference

@idauthorstitledoi/urlcatalogue
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
22702Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29526Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29526)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
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
89892Reimer, 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-ID402767.1