Strain identifier

BacDive ID: 23970

Type strain: Yes

Species: Xenorhabdus khoisanae

Strain Designation: SF87

Strain history: <- C. A. Van Reenen, Dept. Microbiology, Stellenbosch Univ., South Africa; SF87 <- T. Ferreira, Department of Conservation Ecology and Entomology, University of Stellenbosch

NCBI tax ID(s): 880157 (species)

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

@ref: 20910

BacDive-ID: 23970

DSM-Number: 25463

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

description: Xenorhabdus khoisanae SF87 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from nematode Steinernema khoisanae.

NCBI tax id

  • NCBI tax id: 880157
  • Matching level: species

strain history

  • @ref: 20910
  • history: <- C. A. Van Reenen, Dept. Microbiology, Stellenbosch Univ., South Africa; SF87 <- T. Ferreira, Department of Conservation Ecology and Entomology, University of Stellenbosch

doi: 10.13145/bacdive23970.20230509.8.1

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 khoisanae
  • full scientific name: Xenorhabdus khoisanae Ferreira et al. 2013

@ref: 20910

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus khoisanae

full scientific name: Xenorhabdus khoisanae Ferreira et al. 2013

strain designation: SF87

type strain: yes

Morphology

cell morphology

  • @ref: 30988
  • gram stain: negative
  • cell length: 2.5 µm
  • cell width: 0.45 µm
  • cell shape: rod-shaped

pigmentation

  • @ref: 30988
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20910
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

  • @ref: 20910
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30988
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3098824265gluconate+carbon source
3098817234glucose+carbon source
3098817306maltose+carbon source
3098837684mannose+carbon source
30988506227N-acetylglucosamine+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 20910
  • sample type: nematode Steinernema khoisanae
  • host species: Steinernema khoisanae
  • geographic location: Western Cape Province
  • country: South Africa
  • origin.country: ZAF
  • continent: Africa

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3300.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_31;99_3300&stattab=map
  • Last taxonomy: Xenorhabdus
  • 16S sequence: HQ142625
  • Sequence Identity:
  • Total samples: 5
  • aquatic counts: 1
  • animal counts: 4

Safety information

risk assessment

  • @ref: 20910
  • pathogenicity animal: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20910
  • description: Xenorhabdus khoisanae strain SF87 16S ribosomal RNA gene, partial sequence
  • accession: HQ142625
  • length: 1424
  • database: ena
  • NCBI tax ID: 880157

Genome sequences

  • @ref: 66792
  • description: Xenorhabdus khoisanae SF87
  • accession: GCA_028598485
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 880157

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes58.683no
gram-positiveno98.498no
anaerobicno97.794yes
aerobicyes84.933yes
halophileno87.757no
spore-formingno94.162no
glucose-fermentyes86.79no
thermophileno98.968yes
glucose-utilyes92.5no
motileyes90.184no

External links

@ref: 20910

culture collection no.: DSM 25463, ATCC BAA 2406, LMG 29522

straininfo link

  • @ref: 87951
  • straininfo: 404635

literature

  • topic: Phylogeny
  • Pubmed-ID: 23456807
  • title: Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae.
  • authors: Ferreira T, van Reenen CA, Endo A, Sproer C, Malan AP, Dicks LMT
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.049049-0
  • year: 2013
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, South Africa, Xenorhabdus/*classification/genetics/isolation & purification
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20910Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25463Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25463)
30988Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172731828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
87951Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404635.1