Strain identifier

BacDive ID: 5192

Type strain: Yes

Species: Xenorhabdus innexi

Strain Designation: Sca

Strain history: CIP <- 2005, DSMZ <- K. Lengyel <- A. Fodor, univ. Budapest

NCBI tax ID(s): 290109 (species)

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General

@ref: 6373

BacDive-ID: 5192

DSM-Number: 16336

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

description: Xenorhabdus innexi Sca is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from nematode Steinernema scapterisci.

NCBI tax id

  • NCBI tax id: 290109
  • Matching level: species

strain history

@refhistory
6373<- K. Lengyel; Sca <- A. Fodor, Univ. Budapest
120121CIP <- 2005, DSMZ <- K. Lengyel <- A. Fodor, univ. Budapest

doi: 10.13145/bacdive5192.20230509.8.1

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

@ref: 6373

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus innexi

full scientific name: Xenorhabdus innexi Lengyel et al. 2005

strain designation: Sca

type strain: yes

Morphology

cell morphology

  • @ref: 120121
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 120121

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6373CASO 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
120121CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 6373
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120121
  • 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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68369adipate-assimilation17128
68369gluconate+assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369tryptophan+energy source27897
68369nitrate-reduction17632
120121nitrate-reduction17632
120121nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12012135581indoleyes

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+
120121oxidase-
120121alcohol dehydrogenase-1.1.1.1
120121catalase-1.11.1.6
120121lysine decarboxylase-4.1.1.18
120121ornithine decarboxylase-4.1.1.17
120121urease-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
120121--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6373-+-+/--+/-+-+-+-+-++-+--+/-
6373-++++-+-+-+-+-+------
6373-++++-+-+-+-+-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120121+/----+/------+++--------+---------+/---------------+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
6373nematode Steinernema scapterisciSteinernema scapterisciUruguayURYMiddle and South America
120121Other, Nematode Steinernema scapterisciUruguayURYMiddle and South America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_56641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_40407;99_56641&stattab=map
  • Last taxonomy: Xenorhabdus innexi subclade
  • 16S sequence: AJ810292
  • Sequence Identity:
  • Total samples: 249
  • soil counts: 3
  • aquatic counts: 32
  • animal counts: 211
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6373yes1Risk group (German classification)
1201211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Xenorhabdus innexi partial 16S rRNA gene, type strain DSM 16336T
  • accession: AJ810292
  • length: 1529
  • database: ena
  • NCBI tax ID: 290109

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus innexi DSM 16336GCA_002632485scaffoldncbi290109
66792Xenorhabdus innexi strain DSM 16336290109.8wgspatric290109
66792Xenorhabdus innexi DSM 163362895319678draftimg290109

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes67.171no
gram-positiveno98.425no
anaerobicno96.571no
aerobicyes66.081no
halophileno88.863no
spore-formingno93.271no
thermophileno98.56yes
glucose-utilyes87.73yes
motileyes88.49no
glucose-fermentyes81.601no

External links

@ref: 6373

culture collection no.: DSM 16336, CIP 108894, NCIMB 14017, NCIMB 14018

straininfo link

  • @ref: 74684
  • straininfo: 362277

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
Pathogenicity30095261Rhabdopeptide/Xenortide-like Peptides from Xenorhabdus innexi with Terminal Amines Showing Potent Antiprotozoal Activity.Zhao L, Kaiser M, Bode HBOrg Lett10.1021/acs.orglett.8b019752018Amines/*chemistry, Antiprotozoal Agents/*chemistry/*pharmacology, Inhibitory Concentration 50, Leishmania donovani/drug effects, Peptides/*chemistry/*pharmacology, Plasmodium falciparum/drug effects, Xenorhabdus/*chemistry

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6373Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16336)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16336
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
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
74684Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362277.1StrainInfo: A central database for resolving microbial strain identifiers
120121Curators of the CIPCollection of Institut Pasteur (CIP 108894)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108894