Strain identifier

BacDive ID: 5185

Type strain: Yes

Species: Xenorhabdus nematophila

Strain history: CIP <- 2005, CCUG <- 1983, F. Gavini, INSERM, Villeneuve d'Ascq, France <- G.O. Poinar, Jr <- G. M. Thomas

NCBI tax ID(s): 406817 (strain), 628 (species)

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

@ref: 1363

BacDive-ID: 5185

DSM-Number: 3370

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

description: Xenorhabdus nematophila DSM 3370 is an aerobe, mesophilic, motile animal pathogen that was isolated from intestinal lumen of Neoplectana sp..

NCBI tax id

NCBI tax idMatching level
628species
406817strain

strain history

@refhistory
1363<- E. Stackebrandt <- ATCC <- G.O. Poinar, Jr. and G.M.Thomas ("Achromobacter nematophilus")
121262CIP <- 2005, CCUG <- 1983, F. Gavini, INSERM, Villeneuve d'Ascq, France <- G.O. Poinar, Jr <- G. M. Thomas

doi: 10.13145/bacdive5185.20230509.8.1

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
  • full scientific name: Xenorhabdus nematophila corrig. (Poinar and Thomas 1965) Thomas and Poinar 1979 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Xenorhabdus nematophilus
    20215Achromobacter nematophilus

@ref: 1363

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus nematophila

full scientific name: Xenorhabdus nematophila (Poinar and Thomas 1965) Thomas and Poinar 1979

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.526
6948099.874negative
121262yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1363REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
121262CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1363positivegrowth26mesophilic
46042positivegrowth30mesophilic
46042positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46042aerobe
46042microaerophile
121262facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.553

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836927897tryptophan-energy source
6836917632nitrate-reduction
12126217632nitrate-reduction
12126216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12126235581indoleno

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
121262oxidase-
121262alcohol dehydrogenase-1.1.1.1
121262catalase-1.11.1.6
121262lysine decarboxylase-4.1.1.18
121262ornithine decarboxylase-4.1.1.17
121262urease-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
121262-+++-++---++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1363--+---+-+-+-+--------
1363------+-+-+-+----+-++/-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesisolation date
1363intestinal lumen of Neoplectana sp.Neoplectana
46042Intestinal lumen of Neoaplectana sp.
121262Intestinal lumen DD 136 strain of Neoaplectana carpocapsae Weiser1964

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Nematoda
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1363yes1Risk group (German classification)
1212621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xenorhabdus nematophila gene for 16S rRNA, partial sequence, strain: ATCC 19061D780091479ena628
20218Xenorhabdus nematophila 16S ribosomal RNA gene, partial sequenceAY2786741496ena628
20218X.nematophilus 16S rRNA gene (DSM 3370)X822511497ena628

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus nematophila ATCC 19061GCA_000252955chromosomencbi406817
66792Xenorhabdus nematophila ATCC 19061406817.27completepatric406817
66792Xenorhabdus nematophila ATCC 19061406817.32plasmidpatric406817
66792Xenorhabdus nematophila ATCC 19061649633108completeimg406817

GC content

  • @ref: 1363
  • GC-content: 43.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.139no
anaerobicno97.357yes
halophileno89.67no
spore-formingno92.143no
glucose-utilyes90.418yes
aerobicyes76.116no
flagellatedyes55.778no
motileyes87.909no
thermophileno98.167no
glucose-fermentyes84.799no

External links

@ref: 1363

culture collection no.: DSM 3370, ATCC 19061, CCM 7081, CCUG 14189, CIP 108994, LMG 1036, CUETM 8319

straininfo link

  • @ref: 74677
  • straininfo: 6427

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
16348462Characterization of Tn5-Induced Mutants of Xenorhabdus nematophilus ATCC 19061.Xu J, Olson ME, Kahn ML, Hurlbert REAppl Environ Microbiol10.1128/aem.57.4.1173-1180.19911991
22125637The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Leon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Medigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair HPLoS One10.1371/journal.pone.00279092011PhylogenyAnimals, Chromosomes, Bacterial/genetics, DNA, Bacterial/chemistry/genetics, Enterobacteriaceae/classification/genetics/physiology, *Genetic Variation, Genome, Bacterial/*genetics, Genomics/methods, Host-Parasite Interactions, Host-Pathogen Interactions, Insecta/microbiology/parasitology, Molecular Sequence Data, Nematoda/microbiology/physiology, Photorhabdus/classification/*genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Symbiosis, Xenorhabdus/classification/*genetics/physiologyGenetics
30114602TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila.Yadav M, Rathore JSComput Biol Chem10.1016/j.compbiolchem.2018.07.0102018GeneticsBacterial Proteins/*genetics, Bacterial Toxins/*genetics, Genomics, Photorhabdus/genetics, Phylogeny, Toxin-Antitoxin Systems/*genetics, Xenorhabdus/*geneticsPhylogeny
30919769Characteristics and Function of the Chitin Binding Protein from Xenorhabdus nematophila.Liu J, Song P, Zhang J, Nangong Z, Liu X, Gao Y, Wang QProtein Pept Lett10.2174/09298665266661903271433352019PathogenicityAnimals, Antifungal Agents/*chemistry/pharmacology, Ascomycota/drug effects, Bacterial Proteins/*chemistry/genetics/pharmacology, Carrier Proteins/*chemistry/genetics/pharmacology, Chitin/*chemistry, Escherichia coli/genetics, Insecticides/chemistry, Larva/drug effects, Moths/drug effects, Protein Binding, Xenorhabdus/*chemistry
32422264Novel insecticidal chitinase from the insect pathogen Xenorhabdus nematophila.Mahmood S, Kumar M, Kumari P, Mahapatro GK, Banerjee N, Sarin NBInt J Biol Macromol10.1016/j.ijbiomac.2020.05.0782020EnzymologyChemical Phenomena, Chitinases/*chemistry/genetics/isolation & purification/*pharmacology, Circular Dichroism, Cloning, Molecular, Dose-Response Relationship, Drug, Gene Expression, Insecticides/*chemistry/*pharmacology, Models, Biological, Protein Conformation, Recombinant Proteins, Sequence Analysis, DNA, Spectrum Analysis, Xenorhabdus/*enzymology/geneticsTranscriptome
34839000Functional and transcriptional analysis of chromosomal encoded hipBA(Xn2) type II toxin-antitoxin (TA) module from Xenorhabdus nematophila.Yadav M, Rathore JSMicrob Pathog10.1016/j.micpath.2021.1053092021Pathogenicity*Antitoxins/genetics, Bacterial Proteins/genetics, DNA-Binding Proteins, Escherichia coli/genetics, *Escherichia coli Proteins, *Toxin-Antitoxin Systems/genetics, *Xenorhabdus/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1363Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3370)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3370
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
46042Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14189)https://www.ccug.se/strain?id=14189
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
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
74677Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID6427.1StrainInfo: A central database for resolving microbial strain identifiers
121262Curators of the CIPCollection of Institut Pasteur (CIP 108994)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108994