Strain identifier
BacDive ID: 5208
Type strain:
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)
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
@ref | history |
---|---|
16256 | <- P. Tailliez, INRA, Univ. Montpellier, France; VN01 <- N. E. Boemare <- F. Stock <- S. Pagès |
123839 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.943 | ||
69480 | 99.953 | negative | ||
123839 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16256 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
37880 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123839 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16256 | positive | growth | 28 | mesophilic |
37880 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 123839
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.434 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123839 | 17632 | nitrate | - | reduction |
123839 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 123839
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
123839 | oxidase | - | |
123839 | catalase | + | 1.11.1.6 |
123839 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123839 | - | + | - | + | - | + | + | - | + | - | + | + | - | - | - | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
16256 | nematode Steinernema sangi | Steinernema sangi | Vietnam | VNM | Asia | |
123839 | Animal, Nematode, Steinernema sangi | Vietnam | VNM | Asia | 2004 |
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Nematoda
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
16256 | yes | 1 | Risk group (German classification) |
123839 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xenorhabdus vietnamensis DSM 22392 | GCA_002127535 | scaffold | ncbi | 351656 |
66792 | Xenorhabdus vietnamensis strain DSM 22392 | 351656.5 | wgs | patric | 351656 |
66792 | Xenorhabdus vietnamensis DSM 22392 | 2895364164 | draft | img | 351656 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 57.235 | no |
gram-positive | no | 98.441 | no |
anaerobic | no | 98.109 | no |
halophile | no | 87.05 | no |
spore-forming | no | 94.102 | no |
glucose-util | yes | 90.87 | no |
aerobic | yes | 86.233 | no |
thermophile | no | 98.688 | yes |
motile | yes | 89.235 | no |
glucose-ferment | yes | 86.927 | no |
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
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
16256 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22392) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22392 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
37880 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7746 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
74700 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID370416.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
123839 | Curators of the CIP | Collection of Institut Pasteur (CIP 109945) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109945 |