Strain identifier

BacDive ID: 5202

Type strain: Yes

Species: Xenorhabdus kozodoii

Strain Designation: SaV

Strain history: CIP <- 2004, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain Sav

NCBI tax ID(s): 351676 (species)

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General

@ref: 7238

BacDive-ID: 5202

DSM-Number: 17907

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

description: Xenorhabdus kozodoii SaV is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema arenarium .

NCBI tax id

  • NCBI tax id: 351676
  • Matching level: species

strain history

@refhistory
7238<- P. Tailliez; SaV <- N. E. Boemare <- R. Akhurst <- Veremchuck, St. Petersburg
374642004, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain Sav
120497CIP <- 2004, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain Sav

doi: 10.13145/bacdive5202.20230509.8.1

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

@ref: 7238

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus kozodoii

full scientific name: Xenorhabdus kozodoii Tailliez et al. 2006

strain designation: SaV

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.471
6948099.961negative
120497yesnegativerod-shaped

colony morphology

  • @ref: 120497
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7238TRYPTICASE 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
37464MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120497CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7238positivegrowth28mesophilic
37464positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120497
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.946

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
120497nitrate-reduction17632
120497nitrite-reduction16301

metabolite production

  • @ref: 120497
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
120497oxidase-
120497alcohol dehydrogenase-1.1.1.1
120497catalase-1.11.1.6
120497lysine decarboxylase-4.1.1.18
120497ornithine decarboxylase-4.1.1.17
120497urease-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
120497-+++-++---++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120497+/----+/------++/-+--------+-----+---+--------------+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
7238Steinernema arenarium (S. anomalae)Steinernema arenarium;Steinernema anomalaeVoronezRussiaRUSEurope
120497Animal, Nematode Steinernema arenarium, anamalaeVoronezhRussian FederationRUSEurope1986

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7238yes1Risk group (German classification)
1204971Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7238
  • description: Xenorhabdus kozodoii strain SaV 16S ribosomal RNA gene, partial sequence
  • accession: DQ211716
  • length: 1482
  • database: ena
  • NCBI tax ID: 351676

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus kozodoii DSM 17907GCA_002632875scaffoldncbi351676
66792Xenorhabdus kozodoii strain DSM 17907351676.4wgspatric351676

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes63.478no
gram-positiveno98.209no
anaerobicno97.562no
aerobicyes82.795no
halophileno87.335no
spore-formingno93.628no
glucose-utilyes92.328no
thermophileno98.294no
motileyes90.822no
glucose-fermentyes86.676no

External links

@ref: 7238

culture collection no.: DSM 17907, CIP 109068

straininfo link

  • @ref: 74694
  • straininfo: 297371

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
7238Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17907)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17907
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
37464Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6768
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)
68371Automatically annotated from API 50CH acid
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
74694Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297371.1StrainInfo: A central database for resolving microbial strain identifiers
120497Curators of the CIPCollection of Institut Pasteur (CIP 109068)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109068