Strain identifier

BacDive ID: 5200

Type strain: Yes

Species: Xenorhabdus stockiae

Strain Designation: TH01

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain TH01

NCBI tax ID(s): 351614 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7235

BacDive-ID: 5200

DSM-Number: 17904

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

description: Xenorhabdus stockiae TH01 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema siamkayai.

NCBI tax id

  • NCBI tax id: 351614
  • Matching level: species

strain history

@refhistory
7235<- P. Tailliez; TH01 <- N. E. Boemare <- S. Pagès
123321CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain TH01

doi: 10.13145/bacdive5200.20230509.8.1

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

@ref: 7235

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus stockiae

full scientific name: Xenorhabdus stockiae Tailliez et al. 2006

strain designation: TH01

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.366
6948099.961negative
123321yesnegativerod-shaped

colony morphology

  • @ref: 123321

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7235TRYPTICASE 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
123321CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 7235
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123321
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.933

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12332117632nitrate-reduction
12332116301nitrite-reduction

metabolite production

  • @ref: 123321
  • 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
123321oxidase-
123321alcohol dehydrogenase-1.1.1.1
123321catalase-1.11.1.6
123321lysine decarboxylase-4.1.1.18
123321ornithine decarboxylase-4.1.1.17
123321urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123321-+++-+----++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7235Steinernema siamkayaiSteinernema siamkayaiThailandTHAAsia
123321Animal, Nematode Steinernema siamkayaiThailandTHAAsia2000

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_26107.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_19608;99_26107&stattab=map
  • Last taxonomy: Xenorhabdus stockiae subclade
  • 16S sequence: DQ202309
  • Sequence Identity:
  • Total samples: 494
  • soil counts: 23
  • aquatic counts: 45
  • animal counts: 420
  • plant counts: 6

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7235yes1Risk group (German classification)
1233211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7235
  • description: Xenorhabdus stockiae strain TH01 16S ribosomal RNA gene, partial sequence
  • accession: DQ202309
  • length: 1478
  • database: ena
  • NCBI tax ID: 351614

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus stockiae DSM 17904GCA_002632825scaffoldncbi351614
66792Xenorhabdus stockiae strain DSM 17904351614.4wgspatric351614
66792Xenorhabdus stockiae DSM 179042897671627draftimg351614

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes55.938no
gram-positiveno98.249no
anaerobicno96.326no
aerobicyes66.308no
halophileno87.16no
spore-formingno94.097no
glucose-utilyes86.982no
thermophileno98.092yes
motileyes86.671no
glucose-fermentyes80.871no

External links

@ref: 7235

culture collection no.: DSM 17904, CIP 109067

straininfo link

  • @ref: 74692
  • straininfo: 297376

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/urltitlejournalpubmed
7235Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17904)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17904
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)
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
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
74692Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297376.1StrainInfo: A central database for resolving microbial strain identifiers
123321Curators of the CIPCollection of Institut Pasteur (CIP 109067)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109067