Strain identifier

BacDive ID: 5206

Type strain: Yes

Species: Xenorhabdus griffiniae

Strain Designation: ID10

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain ID10

NCBI tax ID(s): 351672 (species)

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General

@ref: 7242

BacDive-ID: 5206

DSM-Number: 17911

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

description: Xenorhabdus griffiniae ID10 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from Steinernema hermaphroditum.

NCBI tax id

  • NCBI tax id: 351672
  • Matching level: species

strain history

@refhistory
7242<- P. Tailliez; ID10 <- N. E. Boemare <- S. Pagès
383802005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain ID10
119739CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain ID10

doi: 10.13145/bacdive5206.20230509.8.1

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

@ref: 7242

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus griffiniae

full scientific name: Xenorhabdus griffiniae Tailliez et al. 2006

strain designation: ID10

type strain: yes

Morphology

cell morphology

  • @ref: 119739
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7242TRYPTICASE 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
38380MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119739CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7242positivegrowth30mesophilic
38380positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119739
  • oxygen tolerance: facultative anaerobe

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
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
68369malate+assimilation25115
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
68369arginine+hydrolysis29016
68369D-glucose+fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368ornithine+degradation18257
68368lysine+degradation25094
68368arginine+hydrolysis29016
119739nitrate-reduction17632
119739nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11973935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

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
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase+3.5.3.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
119739oxidase-
119739alcohol dehydrogenase-1.1.1.1
119739catalase-1.11.1.6
119739lysine decarboxylase-4.1.1.18
119739ornithine decarboxylase-4.1.1.17
119739urease-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
119739-+---++-+-++---+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7242-++++-----++---------
7242-+++------++++++++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7242--+++++++-+-+++--++--
7242--++-++-+-+-+++--+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119739+/----+/------++/-+--------+-----+/----------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7242Steinernema hermaphroditumSteinernema hermaphroditumIndonesiaIDNAsia
119739Animal, Nematode Steinernema hermaphroditumIndonesiaIDNAsia2004

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7242yes1Risk group (German classification)
1197391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7242
  • description: Xenorhabdus griffiniae strain ID10 16S ribosomal RNA gene, partial sequence
  • accession: DQ211710
  • length: 1473
  • database: ena
  • NCBI tax ID: 351672

Genome sequences

  • @ref: 66792
  • description: Xenorhabdus griffiniae ID10
  • accession: GCA_028598495
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 351672

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes56.849no
gram-positiveno98.235no
anaerobicno97.854no
aerobicyes84.568no
halophileno85.135no
spore-formingno94.028no
glucose-fermentyes87.428yes
thermophileno96.926no
glucose-utilyes91.601no
motileyes88.856no

External links

@ref: 7242

culture collection no.: DSM 17911, CIP 109073

straininfo link

  • @ref: 74698
  • straininfo: 297368

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
7242Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17911)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17911
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
38380Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6774
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)
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74698Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297368.1StrainInfo: A central database for resolving microbial strain identifiers
119739Curators of the CIPCollection of Institut Pasteur (CIP 109073)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109073