Strain identifier

BacDive ID: 5204

Type strain: Yes

Species: Xenorhabdus doucetiae

Strain Designation: FRM16

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain FRM16

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

@ref: 7240

BacDive-ID: 5204

DSM-Number: 17909

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

description: Xenorhabdus doucetiae FRM16 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema diaprepesi.

NCBI tax id

NCBI tax idMatching level
351671species
1123505strain

strain history

@refhistory
7240<- P. Tailliez; FRM16 <- N. E. Boemare <- M. Fischer-Le Saux
118968CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain FRM16

doi: 10.13145/bacdive5204.20230509.8.1

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

@ref: 7240

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus doucetiae

full scientific name: Xenorhabdus doucetiae Tailliez et al. 2006

strain designation: FRM16

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.961
6948099.926negative
118968yesnegativerod-shaped

colony morphology

  • @ref: 118968

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7240TRYPTICASE 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
118968CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 7240
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118968
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no98.967

compound production

  • @ref: 7240
  • compound: xenoamicins

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11896817632nitrate-reduction
11896816301nitrite-reduction

metabolite production

  • @ref: 118968
  • 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
118968oxidase-
118968alcohol dehydrogenase-1.1.1.1
118968catalase-1.11.1.6
118968lysine decarboxylase-4.1.1.18
118968ornithine decarboxylase-4.1.1.17
118968urease-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
118968-+++-++---++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
7240Steinernema diaprepesiSteinernema diaprepesiMartinique IslandFranceFRAEurope
118968Animal, Nematode Steinernema diaprepesiMartiniqueFranceFRAEurope1994

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_637.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_516;99_637&stattab=map
  • Last taxonomy: Xenorhabdus doucetiae
  • 16S sequence: DQ211709
  • Sequence Identity:
  • Total samples: 112
  • soil counts: 19
  • aquatic counts: 9
  • animal counts: 76
  • plant counts: 8

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7240yes1Risk group (German classification)
1189681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7240
  • description: Xenorhabdus doucetiae strain FRM16 16S ribosomal RNA gene, partial sequence
  • accession: DQ211709
  • length: 1487
  • database: ena
  • NCBI tax ID: 1123505

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus doucetiae FRM16GCA_000968195completencbi351671
66792Xenorhabdus doucetiae DSM 17909GCA_008124675scaffoldncbi351671
66792Xenorhabdus doucetiae strain DSM 17909351671.8wgspatric351671
66792Xenorhabdus doucetiae strain FRM16 = DSM 17909351671.5completepatric351671
66792Xenorhabdus doucetiae DSM 179092599185204draftimg351671
66792Xenorhabdus doucetiae DSM 179092630968576completeimg351671

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.594no
flagellatedyes62.634no
gram-positiveno98.062no
anaerobicno98.224no
aerobicyes76.87no
halophileno85.252no
spore-formingno94.928no
thermophileno98.493yes
glucose-utilyes88.547no
glucose-fermentyes84.637no

External links

@ref: 7240

culture collection no.: DSM 17909, CIP 109074

straininfo link

  • @ref: 74696
  • straininfo: 297366

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
Phylogeny21948091Description of Xenorhabdus magdalenensis sp. nov., the symbiotic bacterium associated with Steinernema australe.Tailliez P, Pages S, Edgington S, Tymo LM, Buddie AGInt J Syst Evol Microbiol10.1099/ijs.0.034322-02011Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, Symbiosis, Xenorhabdus/*classification/genetics/isolation & purificationGenetics
Metabolism24203528Structure and biosynthesis of xenoamicins from entomopathogenic Xenorhabdus.Zhou Q, Grundmann F, Kaiser M, Schiell M, Gaudriault S, Batzer A, Kurz M, Bode HBChemistry10.1002/chem.2013024812013Anti-Bacterial Agents/*chemistry/metabolism/pharmacology, Antifungal Agents/*chemistry/metabolism/pharmacology, Bacteria/drug effects, Bacterial Infections/drug therapy, Biological Products/*chemistry/metabolism/pharmacology, Fungi/drug effects, Humans, Multigene Family, Mycoses/drug therapy, Peptides/*chemistry/genetics/metabolism/pharmacology, Xenorhabdus/*chemistry/genetics/metabolismPathogenicity
Phylogeny27907104A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae.Ogier JC, Duvic B, Lanois A, Givaudan A, Gaudriault SPLoS One10.1371/journal.pone.01674432016Amino Acid Sequence/genetics, Animals, Bacterial Toxins/genetics, Contact Inhibition/*genetics, Escherichia coli Proteins/genetics, Insecta/microbiology, Membrane Proteins/*genetics, Nematoda/microbiology, Phylogeny, Symbiosis/genetics, Xenorhabdus/classification/*genetics/pathogenicityPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7240Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17909)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17909
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
74696Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297366.1StrainInfo: A central database for resolving microbial strain identifiers
118968Curators of the CIPCollection of Institut Pasteur (CIP 109074)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109074