Strain identifier
BacDive ID: 5189
Type strain:
Species: Xenorhabdus japonica
Strain Designation: SK-1
Strain history: CIP <- 2006, DSMZ <- strain: SK-1
NCBI tax ID(s): 53341 (species)
General
@ref: 6387
BacDive-ID: 5189
DSM-Number: 16522
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, animal pathogen
description: Xenorhabdus japonica SK-1 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Steinernema kushidai.
NCBI tax id
- NCBI tax id: 53341
- Matching level: species
strain history
@ref | history |
---|---|
6387 | <- Y. Nishimura; SK-1 |
120317 | CIP <- 2006, DSMZ <- strain: SK-1 |
doi: 10.13145/bacdive5189.20230509.8.1
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 japonica
- full scientific name: Xenorhabdus japonica corrig. Nishimura et al. 1995
synonyms
- @ref: 20215
- synonym: Xenorhabdus japonicus
@ref: 6387
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Morganellaceae
genus: Xenorhabdus
species: Xenorhabdus japonica
full scientific name: Xenorhabdus japonica Nishimura et al. 1995
strain designation: SK-1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 97.835 | ||
69480 | 99.944 | negative | ||
120317 | yes | negative | rod-shaped |
colony morphology
- @ref: 120317
- hemolysis ability: 1
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6387 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
6387 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
36775 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120317 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6387 | positive | growth | 28 | mesophilic |
36775 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120317
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.935 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
68369 | malate | - | assimilation | 25115 |
68369 | decanoate | - | assimilation | 27689 |
68369 | gluconate | - | assimilation | 24265 |
68369 | N-acetylglucosamine | - | assimilation | 59640 |
68369 | D-mannitol | - | assimilation | 16899 |
68369 | L-arabinose | - | assimilation | 30849 |
68369 | gelatin | - | hydrolysis | 5291 |
68369 | esculin | - | hydrolysis | 4853 |
68369 | urea | - | hydrolysis | 16199 |
68369 | arginine | - | hydrolysis | 29016 |
68369 | D-glucose | + | fermentation | 17634 |
68369 | tryptophan | - | energy source | 27897 |
68369 | nitrate | - | reduction | 17632 |
120317 | nitrate | - | reduction | 17632 |
120317 | nitrite | - | reduction | 16301 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
120317 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
120317 | oxidase | - | |
120317 | alcohol dehydrogenase | - | 1.1.1.1 |
120317 | catalase | - | 1.11.1.6 |
120317 | lysine decarboxylase | - | 4.1.1.18 |
120317 | ornithine decarboxylase | - | 4.1.1.17 |
120317 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120317 | - | + | - | - | - | + | + | - | - | - | + | - | - | - | - | + | - | + | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6387 | - | - | + | - | - | - | - | - | +/- | - | +/- | - | - | +/- | - | - | +/- | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120317 | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | +/- | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
6387 | nematode Steinernema kushidai | Steinernema kushidai | Shizuoka Prefecture | Japan | JPN | Asia |
120317 | Other, Nematode Steinernema kushidai | Shizuoka Prefecture | Japan | JPN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Nematoda
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
6387 | yes | 1 | Risk group (German classification) |
120317 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Xenorhabdus japonica strain DSM16522T 16S ribosomal RNA gene, partial sequence | DQ202310 | 1476 | ena | 53341 |
6387 | X.japonicus (strain SK-1T, type strain) 16S rRNA gene | Z76739 | 1389 | ena | 53341 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xenorhabdus japonica DSM 16522 | GCA_900115195 | scaffold | ncbi | 53341 |
66792 | Xenorhabdus japonica strain DSM 16522 | 53341.3 | wgs | patric | 53341 |
66792 | Xenorhabdus japonica DSM 16522 | 2684622846 | draft | img | 53341 |
GC content
- @ref: 6387
- GC-content: 45.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.939 | no |
flagellated | yes | 58.886 | no |
gram-positive | no | 98.536 | no |
anaerobic | no | 98.298 | no |
aerobic | yes | 84.688 | no |
halophile | no | 82.773 | no |
spore-forming | no | 94.991 | no |
glucose-ferment | yes | 88.393 | yes |
thermophile | no | 98.005 | no |
glucose-util | yes | 87.433 | no |
External links
@ref: 6387
culture collection no.: DSM 16522, CIP 108997, IAM 14265
straininfo link
- @ref: 74681
- straininfo: 88058
literature
- topic: Phylogeny
- Pubmed-ID: 24420949
- title: Xenorhabdus japonicus sp. nov. associated with the nematode Steinernema kushidai.
- authors: Nishimura Y, Hagiwara A, Suzuki T, Yamanaka S
- journal: World J Microbiol Biotechnol
- DOI: 10.1007/BF00360889
- year: 1994
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6387 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16522) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16522 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36775 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6690 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68369 | Automatically annotated from API 20NE | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
74681 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88058.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120317 | Curators of the CIP | Collection of Institut Pasteur (CIP 108997) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108997 |