Strain identifier

BacDive ID: 5201

Type strain: Yes

Species: Xenorhabdus cabanillasii

Strain Designation: USTX62

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain USTX62

NCBI tax ID(s): 351673 (species)

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General

@ref: 7236

BacDive-ID: 5201

DSM-Number: 17905

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, animal pathogen

description: Xenorhabdus cabanillasii USTX62 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema riobrave.

NCBI tax id

  • NCBI tax id: 351673
  • Matching level: species

strain history

@refhistory
7236<- P. Tailliez; USTX62 <- N. E. Boemare <- S. Pagès
117085CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain USTX62

doi: 10.13145/bacdive5201.20230509.8.1

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

@ref: 7236

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus cabanillasii

full scientific name: Xenorhabdus cabanillasii Tailliez et al. 2006

strain designation: USTX62

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.742
6948099.941negative
117085nonegativerod-shaped

colony morphology

  • @ref: 117085

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7236TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
117085CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 7236
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117085
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.977

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11708517632nitrate-reduction
11708516301nitrite-reduction

metabolite production

  • @ref: 117085
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
117085oxidase-
117085alcohol dehydrogenase-1.1.1.1
117085catalase-1.11.1.6
117085lysine decarboxylase-4.1.1.18
117085ornithine decarboxylase-4.1.1.17
117085tryptophan deaminase-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117085-+++-++---++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
7236Steinernema riobraveSteinernema riobraveTexasUSAUSANorth America
117085Animal, Nematode Steinernema riobrave SE62TexasUnited States of AmericaUSANorth America1999

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7236yes1Risk group (German classification)
1170851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7236
  • description: Xenorhabdus cabanillasii strain USTX62 16S ribosomal RNA gene, partial sequence
  • accession: AY521244
  • length: 1485
  • database: ena
  • NCBI tax ID: 351673

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus cabanillasii DSM 17905GCA_003386665contigncbi351673
66792Xenorhabdus cabanillasii strain DSM 17905351673.4wgspatric351673
66792Xenorhabdus cabanillasii DSM 179052778260932draftimg351673

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.79no
anaerobicno97.664no
halophileno88.843no
spore-formingno94.627no
glucose-utilyes90.117no
motileyes86.151no
flagellatedno50no
thermophileno97.833yes
aerobicyes79.803no
glucose-fermentyes80.823no

External links

@ref: 7236

culture collection no.: DSM 17905, CIP 109066

straininfo link

  • @ref: 74693
  • straininfo: 297365

literature

  • topic: Phylogeny
  • Pubmed-ID: 17158981
  • title: New insight into diversity in the genus Xenorhabdus, including the description of ten novel species.
  • authors: Tailliez P, Pages S, Ginibre N, Boemare N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64287-0
  • year: 2006
  • mesh: Animals, 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/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
7236Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17905)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17905
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)
68382Automatically annotated from API zym
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
74693Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297365.1StrainInfo: A central database for resolving microbial strain identifiers
117085Curators of the CIPCollection of Institut Pasteur (CIP 109066)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109066