Strain identifier
BacDive ID: 23970
Type strain:
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)
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30988 | 24265 | gluconate | + | carbon source |
30988 | 17234 | glucose | + | carbon source |
30988 | 17306 | maltose | + | carbon source |
30988 | 37684 | mannose | + | carbon source |
30988 | 506227 | N-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
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 58.683 | no |
gram-positive | no | 98.498 | no |
anaerobic | no | 97.794 | yes |
aerobic | yes | 84.933 | yes |
halophile | no | 87.757 | no |
spore-forming | no | 94.162 | no |
glucose-ferment | yes | 86.79 | no |
thermophile | no | 98.968 | yes |
glucose-util | yes | 92.5 | no |
motile | yes | 90.184 | no |
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
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
20910 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25463 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25463) | |||
30988 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27318 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69479 | João 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 beta | https://microbeatlas.org/ | |||
87951 | Reimer, 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 identifiers | 10.60712/SI-ID404635.1 |