Strain identifier

BacDive ID: 5207

Type strain: Yes

Species: Xenorhabdus koppenhoeferi

Strain Designation: USNJ01

Strain history: <- P. Tailliez; USJN01 <- S. Pages

NCBI tax ID(s): 351659 (species)

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General

@ref: 7342

BacDive-ID: 5207

DSM-Number: 18168

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, animal pathogen

description: Xenorhabdus koppenhoeferi USNJ01 is a mesophilic animal pathogen that was isolated from Steinernema scarabaei.

NCBI tax id

  • NCBI tax id: 351659
  • Matching level: species

strain history

  • @ref: 7342
  • history: <- P. Tailliez; USJN01 <- S. Pages

doi: 10.13145/bacdive5207.20230509.8.1

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 koppenhoeferi
  • full scientific name: Xenorhabdus koppenhoeferi Tailliez et al. 2006

@ref: 7342

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus koppenhoeferi

full scientific name: Xenorhabdus koppenhoeferi Tailliez et al. 2006

strain designation: USNJ01

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlink
7342TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf
7342TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

  • @ref: 7342
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-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
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7342------+-+/------------+/-

Isolation, sampling and environmental information

isolation

  • @ref: 7342
  • sample type: Steinernema scarabaei
  • host species: Steinernema scarabaei
  • geographic location: New Jersey
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

Safety information

risk assessment

  • @ref: 7342
  • pathogenicity animal: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7342
  • description: Xenorhabdus koppenhoeferi strain USNJ01 16S ribosomal RNA gene, partial sequence
  • accession: DQ205450
  • length: 1477
  • database: ena
  • NCBI tax ID: 351659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus koppenhoeferi DSM 18168GCA_900116635scaffoldncbi351659
66792Xenorhabdus koppenhoeferi strain DSM 18168351659.4wgspatric351659
66792Xenorhabdus koppenhoeferi DSM 181682684622845draftimg351659

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.523no
flagellatedno52.785no
gram-positiveno97.848no
anaerobicno97.837no
aerobicyes82.688no
halophileno76.282no
spore-formingno94.332no
glucose-fermentyes78.331no
thermophileno94.794no
glucose-utilyes86.351no

External links

@ref: 7342

culture collection no.: DSM 18168, CIP 109199

straininfo link

  • @ref: 74699
  • straininfo: 297370

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158981New insight into diversity in the genus Xenorhabdus, including the description of ten novel species.Tailliez P, Pages S, Ginibre N, Boemare NInt J Syst Evol Microbiol10.1099/ijs.0.64287-02006Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S, Rhabditida/classification/*microbiology, Sequence Analysis, DNA, *Symbiosis, Xenorhabdus/*classification/geneticsGenetics
Phylogeny34898417Xenorhabdus lircayensis sp. nov., the symbiotic bacterium associated with the entomopathogenic nematode Steinernema unicornum.Castaneda-Alvarez C, Prodan S, Zamorano A, San-Blas E, Aballay EInt J Syst Evol Microbiol10.1099/ijsem.0.0051512021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhabditida/microbiology, Sequence Analysis, DNA, *Xenorhabdus/classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7342Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18168)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18168
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
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)
68369Automatically annotated from API 20NE
74699Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297370.1StrainInfo: A central database for resolving microbial strain identifiers