Strain identifier

BacDive ID: 5208

Type strain: Yes

Species: Xenorhabdus vietnamensis

Strain Designation: VN01

Strain history: CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain VN01

NCBI tax ID(s): 351656 (species)

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

@ref: 16256

BacDive-ID: 5208

DSM-Number: 22392

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

description: Xenorhabdus vietnamensis VN01 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema sangi.

NCBI tax id

  • NCBI tax id: 351656
  • Matching level: species

strain history

@refhistory
16256<- P. Tailliez, INRA, Univ. Montpellier, France; VN01 <- N. E. Boemare <- F. Stock <- S. Pagès
123839CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain VN01

doi: 10.13145/bacdive5208.20230509.8.1

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 vietnamensis
  • full scientific name: Xenorhabdus vietnamensis Tailliez et al. 2010

@ref: 16256

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus vietnamensis

full scientific name: Xenorhabdus vietnamensis Tailliez et al. 2010

strain designation: VN01

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.943
6948099.953negative
123839yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16256TRYPTICASE 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
37880MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123839CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16256positivegrowth28mesophilic
37880positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123839
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.434

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12383917632nitrate-reduction
12383916301nitrite-reduction

metabolite production

  • @ref: 123839
  • 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
123839oxidase-
123839catalase+1.11.1.6
123839urease-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
123839-+-+-++-+-++---+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
16256nematode Steinernema sangiSteinernema sangiVietnamVNMAsia
123839Animal, Nematode, Steinernema sangiVietnamVNMAsia2004

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16256yes1Risk group (German classification)
1238391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16256
  • description: Xenorhabdus sp. VN01 16S ribosomal RNA gene, partial sequence
  • accession: DQ205447
  • length: 1467
  • database: ena
  • NCBI tax ID: 351656

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus vietnamensis DSM 22392GCA_002127535scaffoldncbi351656
66792Xenorhabdus vietnamensis strain DSM 22392351656.5wgspatric351656
66792Xenorhabdus vietnamensis DSM 223922895364164draftimg351656

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes57.235no
gram-positiveno98.441no
anaerobicno98.109no
halophileno87.05no
spore-formingno94.102no
glucose-utilyes90.87no
aerobicyes86.233no
thermophileno98.688yes
motileyes89.235no
glucose-fermentyes86.927no

External links

@ref: 16256

culture collection no.: DSM 22392, CIP 109945

straininfo link

  • @ref: 74700
  • straininfo: 370416

literature

  • topic: Phylogeny
  • Pubmed-ID: 19783607
  • title: Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. caribbeanensis subsp. nov., P. luminescens subsp. hainanensis subsp. nov., P. temperata subsp. khanii subsp. nov., P. temperata subsp. tasmaniensis subsp. nov., and the reclassification of P. luminescens subsp. thracensis as P. temperata subsp. thracensis comb. nov.
  • authors: Tailliez P, Laroui C, Ginibre N, Paule A, Pages S, Boemare N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014308-0
  • year: 2009
  • mesh: Animals, Bacterial Proteins/*genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nematoda/*microbiology, Photorhabdus/*classification/genetics/*isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Xenorhabdus/*classification/genetics/*isolation & purification
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
16256Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22392)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22392
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
37880Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7746
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
74700Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370416.1StrainInfo: A central database for resolving microbial strain identifiers
123839Curators of the CIPCollection of Institut Pasteur (CIP 109945)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109945