Strain identifier

BacDive ID: 5193

Type strain: Yes

Species: Xenorhabdus budapestensis

Strain Designation: Bic

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

NCBI tax ID(s): 290110 (species)

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General

@ref: 6396

BacDive-ID: 5193

DSM-Number: 16342

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

description: Xenorhabdus budapestensis Bic is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from nematode Steinernema bicornutum.

NCBI tax id

  • NCBI tax id: 290110
  • Matching level: species

strain history

@refhistory
6396<- K. Lengyel, Bic <- A.Fodor, Univ. Budapest
117075CIP <- 2005, DSMZ <- K. Lengyel, E. L. Univ., Budapest, Hungary <- A. Fodor, E.L. Univ., Budapest, Hungary

doi: 10.13145/bacdive5193.20230509.8.1

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

@ref: 6396

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus budapestensis

full scientific name: Xenorhabdus budapestensis Lengyel et al. 2005

strain designation: Bic

type strain: yes

Morphology

cell morphology

  • @ref: 117075
  • gram stain: negative
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6396CASO 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
38358MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117075CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6396positivegrowth30mesophilic
38358positivegrowth25mesophilic
117075positivegrowth25-37mesophilic
117075nogrowth5psychrophilic
117075nogrowth10psychrophilic
117075nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117075
  • 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
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
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
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
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
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
117075mannitol-fermentation29864
117075citrate-carbon source16947
117075glucose+fermentation17234
117075lactose-fermentation17716
117075nitrate-reduction17632
117075nitrite-reduction16301
117075malonate-assimilation15792
117075sodium thiosulfate-builds gas from132112

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11707535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11707515688acetoin-
11707517234glucose-

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
117075oxidase-
117075beta-galactosidase-3.2.1.23
117075alcohol dehydrogenase-1.1.1.1
117075gelatinase-
117075catalase-1.11.1.6
117075lysine decarboxylase-4.1.1.18
117075ornithine decarboxylase-4.1.1.17
117075phenylalanine ammonia-lyase-4.3.1.24
117075tryptophan deaminase-
117075urease-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
117075-+++-++---++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6396---+/-+/--+-+-+-+----+/---+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117075+/----------+/-+/-+/----+/-----+/------+/----------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
6396nematode Steinernema bicornutumSteinernema bicornutumSerbiaSRBEurope
117075Other, Nematode Steinernema bicormutumSerbiaSRBEuropeSzabadka, Vojvodina

isolation source categories

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

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6396yes1Risk group (German classification)
1170751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Xenorhabdus budapestensis partial 16S rRNA gene, type strain DSM 16342T
  • accession: AJ810293
  • length: 1525
  • database: ena
  • NCBI tax ID: 290110

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus budapestensis DSM 16342GCA_002632465scaffoldncbi290110
66792Xenorhabdus budapestensis strain DSM 16342290110.6wgspatric290110
66792Xenorhabdus budapestensis DSM 163422895349264draftimg290110

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes51.374no
gram-positiveno97.477no
anaerobicno97.672no
aerobicyes76.817no
halophileno83.374no
spore-formingno93.751no
glucose-utilyes90.827yes
thermophileno96.724yes
motileyes87.768no
glucose-fermentyes78.575yes

External links

@ref: 6396

culture collection no.: DSM 16342, CIP 108891, NCIMB 14016

straininfo link

  • @ref: 74685
  • straininfo: 132359

literature

  • topic: Phylogeny
  • Pubmed-ID: 15830803
  • title: Description 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.
  • authors: Lengyel K, Lang E, Fodor A, Szallas E, Schumann P, Stackebrandt E
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2004.10.004
  • year: 2005
  • mesh: Animals, 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/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6396Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16342)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16342
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
38358Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6570
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
74685Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132359.1StrainInfo: A central database for resolving microbial strain identifiers
117075Curators of the CIPCollection of Institut Pasteur (CIP 108891)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108891