Strain identifier

BacDive ID: 5191

Type strain: Yes

Species: Xenorhabdus ehlersii

Strain Designation: Ser

Strain history: CIP <- 2005, DSMZ <- K. Lengyel, E.L. Univ., Budapest, Hungary <- A. Fodor, E.L. Univ., Budapest, Hungary

NCBI tax ID(s): 290111 (species)

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

@ref: 6394

BacDive-ID: 5191

DSM-Number: 16337

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

description: Xenorhabdus ehlersii Ser is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema serratum.

NCBI tax id

  • NCBI tax id: 290111
  • Matching level: species

strain history

@refhistory
6394<- K. Lengyel, Ser <- A. Fodor, Univ. Budapest
119001CIP <- 2005, DSMZ <- K. Lengyel, E.L. Univ., Budapest, Hungary <- A. Fodor, E.L. Univ., Budapest, Hungary

doi: 10.13145/bacdive5191.20230509.8.1

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 ehlersii
  • full scientific name: Xenorhabdus ehlersii Lengyel et al. 2005

@ref: 6394

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus ehlersii

full scientific name: Xenorhabdus ehlersii Lengyel et al. 2005

strain designation: Ser

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes99.076
6948099.935negative
119001yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6394CASO 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
38359MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
38360MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119001CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6394positivegrowth30mesophilic
38359positivegrowth25mesophilic
38360positivegrowth25mesophilic
119001positivegrowth30-37mesophilic
119001nogrowth5psychrophilic
119001nogrowth10psychrophilic
119001nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119001
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.103

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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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-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
68369urea-hydrolysis16199
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
119001mannitol-fermentation29864
119001citrate+carbon source16947
119001glucose+fermentation17234
119001lactose-fermentation17716
119001nitrate-reduction17632
119001nitrite-reduction16301
119001malonate-assimilation15792
119001sodium thiosulfate-builds gas from132112
119001nitrate+respiration17632

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11900135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testmethylred-test
6836935581indole-
11900117234glucose-

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
119001oxidase-
119001beta-galactosidase-3.2.1.23
119001alcohol dehydrogenase-1.1.1.1
119001gelatinase-
119001catalase-1.11.1.6
119001lysine decarboxylase-4.1.1.18
119001ornithine decarboxylase-4.1.1.17
119001phenylalanine ammonia-lyase+4.3.1.24
119001tryptophan deaminase+
119001urease-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
119001-+++-+++--++-+-+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6394---+/--++-+-+-+++--++-+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119001+/----+/------+/-+/-+/---------+/---+/---+/----+/------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
6394nematode Steinernema serratumSteinernema serratumChinaCHNAsia
119001Other, Nematode Steinernema serratumChinaCHNAsiaSouthern China

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_26104.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_5618;99_26104&stattab=map
  • Last taxonomy: Xenorhabdus ehlersii
  • 16S sequence: AJ810294
  • Sequence Identity:
  • Total samples: 3
  • animal counts: 3

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6394yes1Risk group (German classification)
1190011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Xenorhabdus ehlersii partial 16S rRNA gene, type strain DSM 16337T
  • accession: AJ810294
  • length: 1524
  • database: ena
  • NCBI tax ID: 290111

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus ehlersii DSM 16337GCA_003610465contigncbi290111
66792Xenorhabdus ehlersii DSM 16337GCA_002632445scaffoldncbi290111
66792Xenorhabdus ehlersii strain DSM 16337290111.5wgspatric290111
66792Xenorhabdus ehlersii strain DSM 16337290111.6wgspatric290111
66792Xenorhabdus ehlersii DSM 163372772190835draftimg290111

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes59.898no
gram-positiveno98.193no
anaerobicno98.028no
halophileno87.501no
spore-formingno94.406no
glucose-utilyes90.958no
aerobicyes78.634no
thermophileno98.09yes
glucose-fermentyes81.07yes
motileyes89.622no

External links

@ref: 6394

culture collection no.: DSM 16337, CIP 108893, NCIMB 14018

straininfo link

  • @ref: 74683
  • straininfo: 132358

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15830803Description of four novel species of Xenorhabdus, family Enterobacteriaceae: Xenorhabdus budapestensis sp. nov., Xenorhabdus ehlersii sp. nov., Xenorhabdus innexi sp. nov., and Xenorhabdus szentirmaii sp. nov.Lengyel K, Lang E, Fodor A, Szallas E, Schumann P, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.10.0042005Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Enterobacteriaceae/classification, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Ribotyping, Sequence Analysis, DNA, Species Specificity, Symbiosis, Xenorhabdus/*classification/genetics/metabolism/physiologyGenetics
Phylogeny22922533Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari.Kuwata R, Qiu LH, Wang W, Harada Y, Yoshida M, Kondo E, Yoshiga TInt J Syst Evol Microbiol10.1099/ijs.0.041145-02012Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genes, Bacterial, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, Xenorhabdus/*classification/genetics/isolation & purificationGenetics
Phylogeny28056225Xenorhabdus thuongxuanensis sp. nov. and Xenorhabdus eapokensis sp. nov., isolated from Steinernema species.Kampfer P, Tobias NJ, Ke LP, Bode HB, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0017702017Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, Vietnam, Xenorhabdus/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6394Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16337)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16337
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
38359Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6574
38360Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6575
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
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
74683Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132358.1StrainInfo: A central database for resolving microbial strain identifiers
119001Curators of the CIPCollection of Institut Pasteur (CIP 108893)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108893