Strain identifier

BacDive ID: 5199

Type strain: Yes

Species: Xenorhabdus hominickii

Strain Designation: KE01

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain KE01

NCBI tax ID(s): 351679 (species)

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General

@ref: 7234

BacDive-ID: 5199

DSM-Number: 17903

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, animal pathogen

description: Xenorhabdus hominickii KE01 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from Steinernema karii.

NCBI tax id

  • NCBI tax id: 351679
  • Matching level: species

strain history

@refhistory
7234<- P. Tailliez; KE01 <- N. E. Boemare <- S. Pages
119936CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain KE01

doi: 10.13145/bacdive5199.20230509.8.1

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

@ref: 7234

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus hominickii

full scientific name: Xenorhabdus hominickii Tailliez et al. 2006

strain designation: KE01

type strain: yes

Morphology

cell morphology

  • @ref: 119936
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7234TRYPTICASE 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
119936CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 7234
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119936
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1199364853esculin+hydrolysis
11993617632nitrate-reduction
11993616301nitrite-reduction

metabolite production

  • @ref: 119936
  • 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
119936oxidase-
119936catalase-1.11.1.6
119936urease-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
119936--++-+----++-----+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7234Steinernema kariiSteinernema kariiKenyaKENAfrica
119936Animal, Nematode Steinernema kariiKenyaKENAfrica2000

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_31;99_32&stattab=map
  • Last taxonomy: Xenorhabdus
  • 16S sequence: DQ211719
  • Sequence Identity:
  • Total samples: 256
  • soil counts: 20
  • aquatic counts: 14
  • animal counts: 207
  • plant counts: 15

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7234yes1Risk group (German classification)
1199361Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7234
  • description: Xenorhabdus hominickii strain KE01 16S ribosomal RNA gene, partial sequence
  • accession: DQ211719
  • length: 1486
  • database: ena
  • NCBI tax ID: 351679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus hominickii DSM 17903GCA_002632725scaffoldncbi351679
66792Xenorhabdus hominickii strain DSM 17903351679.6wgspatric351679

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes60.389no
gram-positiveno98.381no
anaerobicno98.512no
halophileno86.106no
spore-formingno94.042no
glucose-utilyes88.343no
aerobicyes77.285no
thermophileno98.172yes
motileyes88.458no
glucose-fermentyes82.651no

External links

@ref: 7234

culture collection no.: DSM 17903, CIP 109072

straininfo link

  • @ref: 74691
  • straininfo: 297369

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158981New insight into diversity in the genus Xenorhabdus, including the description of ten novel species.Tailliez P, Pages S, Ginibre N, Boemare NInt J Syst Evol Microbiol10.1099/ijs.0.64287-02006Animals, 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/geneticsGenetics
Phylogeny23456807Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae.Ferreira T, van Reenen CA, Endo A, Sproer C, Malan AP, Dicks LMTInt J Syst Evol Microbiol10.1099/ijs.0.049049-02013Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, South Africa, Xenorhabdus/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitle
7234Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17903)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17903
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
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
74691Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297369.1StrainInfo: A central database for resolving microbial strain identifiers
119936Curators of the CIPCollection of Institut Pasteur (CIP 109072)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109072