Strain identifier

BacDive ID: 5187

Type strain: Yes

Species: Xenorhabdus nematophila subsp. beddingii

Strain Designation: Q 58, Q58

Variant: Isotype of BacDive ID 5188

Strain history: CIP <- 2006, P. Tailliez, INRA, Montpellier, France: strain Q58 <- Boemare <- R. J. Akhurst

NCBI tax ID(s): 40578 (species)

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General

@ref: 1759

BacDive-ID: 5187

DSM-Number: 4764

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

description: Xenorhabdus nematophila subsp. beddingii Q 58 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema sp. M.

NCBI tax id

  • NCBI tax id: 40578
  • Matching level: species

strain history

@refhistory
1759<- UQM
116770CIP <- 2006, P. Tailliez, INRA, Montpellier, France: strain Q58 <- Boemare <- R. J. Akhurst

doi: 10.13145/bacdive5187.20230509.8.1

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 nematophila subsp. beddingii
  • full scientific name: Xenorhabdus nematophila subsp. beddingii corrig. Akhurst 1986

  • synonyms

    @refsynonym
    20215Xenorhabdus nematophilus subsp. beddingii
    20215Xenorhabdus beddingii

@ref: 1759

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus beddingii

full scientific name: Xenorhabdus beddingii (Akhurst 1986) Akhurst and Boemare 1993

strain designation: Q 58, Q58

variant: Isotype of BacDive ID 5188

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.819
6948099.926negative
116770nonegativerod-shaped

colony morphology

  • @ref: 116770

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1759CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
1759XENORHABDUS MEDIUM (DSMZ Medium 423)yeshttps://mediadive.dsmz.de/medium/423Name: XENORHABDUS MEDIUM (DSMZ Medium 423) Composition: Agar 15.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Yeast extract 5.0 g/l Distilled water
34356MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116770CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116770CIP Medium 669yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=669

culture temp

@refgrowthtypetemperaturerange
1759positivegrowth28mesophilic
34356positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116770
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.753

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
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-fructose+builds acid from15824
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
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
116770nitrate-reduction17632
116770nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11677035581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116770oxidase-
116770alcohol dehydrogenase-1.1.1.1
116770catalase-1.11.1.6
116770lysine decarboxylase-4.1.1.18
116770ornithine decarboxylase-4.1.1.17
116770urease-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
116770-+++-++---++---+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1759-----++-+-+-+++--+/---+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116770+---------+++--------+-+/-+/-+/--+---+--------------+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
1759nematode Steinernema sp. MSteinernemaQueenslandAustraliaAUSAustralia and Oceania
116770Animal, Nematode, Steinernema sp.MackayAustraliaAUSAustralia and Oceania1985

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1759yes1Risk group (German classification)
1167701Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xenorhabdus beddingii 16S ribosomal RNA gene, partial sequenceAY2786751497ena40578
20218Xenorhabdus beddingii gene for 16S rRNA, partial sequence, strain: DSM 4764D780061479ena40578
20218X.beddingii 16S rRNA gene (DSM 4764)X822541497ena40578

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus beddingii DSM 4764GCA_002127545scaffoldncbi40578
66792Xenorhabdus beddingii strain DSM 476440578.4wgspatric40578
66792Xenorhabdus beddingii DSM 47642897667629draftimg40578

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes62.547no
gram-positiveno98.25no
anaerobicno97.563no
halophileno85.214no
spore-formingno94.208no
glucose-utilyes89.204no
aerobicyes81.684no
thermophileno98.581no
motileyes88.412no
glucose-fermentyes82.932yes

External links

@ref: 1759

culture collection no.: DSM 4764, ATCC 49542, CCM 7079, UQM 2871, CIP 109145

straininfo link

  • @ref: 74679
  • straininfo: 42541

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1759Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4764)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4764
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34356Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6854
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)
68369Automatically annotated from API 20NE
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
74679Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42541.1StrainInfo: A central database for resolving microbial strain identifiers
116770Curators of the CIPCollection of Institut Pasteur (CIP 109145)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109145