Strain identifier

BacDive ID: 5189

Type strain: Yes

Species: Xenorhabdus japonica

Strain Designation: SK-1

Strain history: CIP <- 2006, DSMZ <- strain: SK-1

NCBI tax ID(s): 53341 (species)

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

@ref: 6387

BacDive-ID: 5189

DSM-Number: 16522

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

description: Xenorhabdus japonica SK-1 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema kushidai.

NCBI tax id

  • NCBI tax id: 53341
  • Matching level: species

strain history

@refhistory
6387<- Y. Nishimura; SK-1
120317CIP <- 2006, DSMZ <- strain: SK-1

doi: 10.13145/bacdive5189.20230509.8.1

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 japonica
  • full scientific name: Xenorhabdus japonica corrig. Nishimura et al. 1995
  • synonyms

    • @ref: 20215
    • synonym: Xenorhabdus japonicus

@ref: 6387

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus japonica

full scientific name: Xenorhabdus japonica Nishimura et al. 1995

strain designation: SK-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.835
6948099.944negative
120317yesnegativerod-shaped

colony morphology

  • @ref: 120317
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6387TRYPTICASE 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
6387CASO 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
36775MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120317CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6387positivegrowth28mesophilic
36775positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120317
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.935

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-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
68369malate-assimilation25115
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369L-arabinose-assimilation30849
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose+fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
120317nitrate-reduction17632
120317nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12031735581indoleno

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
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120317oxidase-
120317alcohol dehydrogenase-1.1.1.1
120317catalase-1.11.1.6
120317lysine decarboxylase-4.1.1.18
120317ornithine decarboxylase-4.1.1.17
120317urease-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
120317-+---++---+----+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6387--+-----+/--+/---+/---+/-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120317----------+++--------+-----+/----+-----------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6387nematode Steinernema kushidaiSteinernema kushidaiShizuoka PrefectureJapanJPNAsia
120317Other, Nematode Steinernema kushidaiShizuoka PrefectureJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6387yes1Risk group (German classification)
1203171Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xenorhabdus japonica strain DSM16522T 16S ribosomal RNA gene, partial sequenceDQ2023101476ena53341
6387X.japonicus (strain SK-1T, type strain) 16S rRNA geneZ767391389ena53341

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus japonica DSM 16522GCA_900115195scaffoldncbi53341
66792Xenorhabdus japonica strain DSM 1652253341.3wgspatric53341
66792Xenorhabdus japonica DSM 165222684622846draftimg53341

GC content

  • @ref: 6387
  • GC-content: 45.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.939no
flagellatedyes58.886no
gram-positiveno98.536no
anaerobicno98.298no
aerobicyes84.688no
halophileno82.773no
spore-formingno94.991no
glucose-fermentyes88.393yes
thermophileno98.005no
glucose-utilyes87.433no

External links

@ref: 6387

culture collection no.: DSM 16522, CIP 108997, IAM 14265

straininfo link

  • @ref: 74681
  • straininfo: 88058

literature

  • topic: Phylogeny
  • Pubmed-ID: 24420949
  • title: Xenorhabdus japonicus sp. nov. associated with the nematode Steinernema kushidai.
  • authors: Nishimura Y, Hagiwara A, Suzuki T, Yamanaka S
  • journal: World J Microbiol Biotechnol
  • DOI: 10.1007/BF00360889
  • year: 1994

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6387Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16522)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16522
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
36775Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6690
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
74681Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88058.1StrainInfo: A central database for resolving microbial strain identifiers
120317Curators of the CIPCollection of Institut Pasteur (CIP 108997)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108997