Strain identifier

BacDive ID: 23011

Type strain: Yes

Species: Xenorhabdus ishibashii

Strain Designation: GDh7

Strain history: <- L. Qiu, State Key Lab. for Biocontrol, Sun Yat-sen Univ., Guangzhou, People's Republic of China; GDh7

NCBI tax ID(s): 1034471 (species)

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General

@ref: 19311

BacDive-ID: 23011

DSM-Number: 22670

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, animal pathogen

description: Xenorhabdus ishibashii GDh7 is a facultative anaerobe, Gram-negative, motile animal pathogen that was isolated from infective nematode juveniles of Steinernema aciari.

NCBI tax id

  • NCBI tax id: 1034471
  • Matching level: species

strain history

  • @ref: 19311
  • history: <- L. Qiu, State Key Lab. for Biocontrol, Sun Yat-sen Univ., Guangzhou, People's Republic of China; GDh7

doi: 10.13145/bacdive23011.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Xenorhabdus
  • species: Xenorhabdus ishibashii
  • full scientific name: Xenorhabdus ishibashii Kuwata et al. 2013

@ref: 19311

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus ishibashii

full scientific name: Xenorhabdus ishibashii Kuwata et al. 2013

strain designation: GDh7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30650negative3.1 µm0.75 µmrod-shapedyes
69480negative100

pigmentation

  • @ref: 30650
  • production: yes

multimedia

  • @ref: 19311
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22670.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 19311
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
19311positivegrowth28
30650positivegrowth37-42

Physiology and metabolism

oxygen tolerance

  • @ref: 30650
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69480no91.282
69481no100

observation

  • @ref: 30650
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3065030089acetate+carbon source
3065016236ethanol+carbon source
306505417glucosamine+carbon source
3065015792malonate+carbon source
306504853esculin+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
6836927897tryptophan-energy source
6836917632nitrate-reduction
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
6836935581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
30650gelatinase+
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
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
19311-++++----+++---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
19311---++++-+-+-+++--++--
19311--+--++-+-+-+++--++--

Isolation, sampling and environmental information

isolation

  • @ref: 19311
  • sample type: infective nematode juveniles of Steinernema aciari
  • host species: Steinernema aciari
  • geographic location: Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Invertebrates (Other)#Nematoda

Safety information

risk assessment

  • @ref: 19311
  • pathogenicity animal: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19311
  • description: Xenorhabdus ishibashii strain GDh7 16S ribosomal RNA gene, partial sequence
  • accession: GQ149086
  • length: 1480
  • database: nuccore
  • NCBI tax ID: 1034471

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus ishibashii DSM 22670GCA_002632755scaffoldncbi1034471
66792Xenorhabdus ishibashii strain DSM 226701034471.3wgspatric1034471
66792Xenorhabdus ishibashii DSM 226702839585306draftimg1034471

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno100no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.635yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no67.78yes
69480spore-formingspore-formingAbility to form endo- or exosporesno91.282no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99no
69480flagellatedmotile2+Ability to perform flagellated movementyes77.031no

External links

@ref: 19311

culture collection no.: DSM 22670, CGMCC 1.9166

straininfo link

  • @ref: 87251
  • straininfo: 388284

literature

  • topic: Phylogeny
  • Pubmed-ID: 22922533
  • title: Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari.
  • authors: Kuwata R, Qiu LH, Wang W, Harada Y, Yoshida M, Kondo E, Yoshiga T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041145-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genes, Bacterial, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, Xenorhabdus/*classification/genetics/isolation & purification
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19311Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22670)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22670
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
30650Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2698128776041
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)
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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
87251Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID388284.1StrainInfo: A central database for resolving microbial strain identifiers