Strain identifier
BacDive ID: 5204
Type strain:
Species: Xenorhabdus doucetiae
Strain Designation: FRM16
Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain FRM16
NCBI tax ID(s): 1123505 (strain), 351671 (species)
General
@ref: 7240
BacDive-ID: 5204
DSM-Number: 17909
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, animal pathogen
description: Xenorhabdus doucetiae FRM16 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema diaprepesi.
NCBI tax id
NCBI tax id | Matching level |
---|---|
351671 | species |
1123505 | strain |
strain history
@ref | history |
---|---|
7240 | <- P. Tailliez; FRM16 <- N. E. Boemare <- M. Fischer-Le Saux |
118968 | CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain FRM16 |
doi: 10.13145/bacdive5204.20230509.8.1
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 doucetiae
- full scientific name: Xenorhabdus doucetiae Tailliez et al. 2006
@ref: 7240
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Morganellaceae
genus: Xenorhabdus
species: Xenorhabdus doucetiae
full scientific name: Xenorhabdus doucetiae Tailliez et al. 2006
strain designation: FRM16
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.961 | ||
69480 | 99.926 | negative | ||
118968 | yes | negative | rod-shaped |
colony morphology
- @ref: 118968
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7240 | 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 |
118968 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
- @ref: 7240
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 118968
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 98.967 |
compound production
- @ref: 7240
- compound: xenoamicins
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118968 | 17632 | nitrate | - | reduction |
118968 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118968
- Chebi-ID: 35581
- metabolite: indole
- production: no
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 |
118968 | oxidase | - | |
118968 | alcohol dehydrogenase | - | 1.1.1.1 |
118968 | catalase | - | 1.11.1.6 |
118968 | lysine decarboxylase | - | 4.1.1.18 |
118968 | ornithine decarboxylase | - | 4.1.1.17 |
118968 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118968 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|---|
7240 | Steinernema diaprepesi | Steinernema diaprepesi | Martinique Island | France | FRA | Europe | |
118968 | Animal, Nematode Steinernema diaprepesi | Martinique | France | FRA | Europe | 1994 |
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Nematoda
taxonmaps
- @ref: 69479
- File name: preview.99_637.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_28;98_516;99_637&stattab=map
- Last taxonomy: Xenorhabdus doucetiae
- 16S sequence: DQ211709
- Sequence Identity:
- Total samples: 112
- soil counts: 19
- aquatic counts: 9
- animal counts: 76
- plant counts: 8
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
7240 | yes | 1 | Risk group (German classification) |
118968 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7240
- description: Xenorhabdus doucetiae strain FRM16 16S ribosomal RNA gene, partial sequence
- accession: DQ211709
- length: 1487
- database: ena
- NCBI tax ID: 1123505
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xenorhabdus doucetiae FRM16 | GCA_000968195 | complete | ncbi | 351671 |
66792 | Xenorhabdus doucetiae DSM 17909 | GCA_008124675 | scaffold | ncbi | 351671 |
66792 | Xenorhabdus doucetiae strain DSM 17909 | 351671.8 | wgs | patric | 351671 |
66792 | Xenorhabdus doucetiae strain FRM16 = DSM 17909 | 351671.5 | complete | patric | 351671 |
66792 | Xenorhabdus doucetiae DSM 17909 | 2599185204 | draft | img | 351671 |
66792 | Xenorhabdus doucetiae DSM 17909 | 2630968576 | complete | img | 351671 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.594 | no |
flagellated | yes | 62.634 | no |
gram-positive | no | 98.062 | no |
anaerobic | no | 98.224 | no |
aerobic | yes | 76.87 | no |
halophile | no | 85.252 | no |
spore-forming | no | 94.928 | no |
thermophile | no | 98.493 | yes |
glucose-util | yes | 88.547 | no |
glucose-ferment | yes | 84.637 | no |
External links
@ref: 7240
culture collection no.: DSM 17909, CIP 109074
straininfo link
- @ref: 74696
- straininfo: 297366
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17158981 | New insight into diversity in the genus Xenorhabdus, including the description of ten novel species. | Tailliez P, Pages S, Ginibre N, Boemare N | Int J Syst Evol Microbiol | 10.1099/ijs.0.64287-0 | 2006 | Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S, Rhabditida/classification/*microbiology, Sequence Analysis, DNA, *Symbiosis, Xenorhabdus/*classification/genetics | Genetics |
Phylogeny | 21948091 | Description of Xenorhabdus magdalenensis sp. nov., the symbiotic bacterium associated with Steinernema australe. | Tailliez P, Pages S, Edgington S, Tymo LM, Buddie AG | Int J Syst Evol Microbiol | 10.1099/ijs.0.034322-0 | 2011 | Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditida/*microbiology, Sequence Analysis, DNA, Symbiosis, Xenorhabdus/*classification/genetics/isolation & purification | Genetics |
Metabolism | 24203528 | Structure and biosynthesis of xenoamicins from entomopathogenic Xenorhabdus. | Zhou Q, Grundmann F, Kaiser M, Schiell M, Gaudriault S, Batzer A, Kurz M, Bode HB | Chemistry | 10.1002/chem.201302481 | 2013 | Anti-Bacterial Agents/*chemistry/metabolism/pharmacology, Antifungal Agents/*chemistry/metabolism/pharmacology, Bacteria/drug effects, Bacterial Infections/drug therapy, Biological Products/*chemistry/metabolism/pharmacology, Fungi/drug effects, Humans, Multigene Family, Mycoses/drug therapy, Peptides/*chemistry/genetics/metabolism/pharmacology, Xenorhabdus/*chemistry/genetics/metabolism | Pathogenicity |
Phylogeny | 27907104 | A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae. | Ogier JC, Duvic B, Lanois A, Givaudan A, Gaudriault S | PLoS One | 10.1371/journal.pone.0167443 | 2016 | Amino Acid Sequence/genetics, Animals, Bacterial Toxins/genetics, Contact Inhibition/*genetics, Escherichia coli Proteins/genetics, Insecta/microbiology, Membrane Proteins/*genetics, Nematoda/microbiology, Phylogeny, Symbiosis/genetics, Xenorhabdus/classification/*genetics/pathogenicity | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7240 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17909) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17909 | |||
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 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68382 | Automatically annotated from API zym | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
74696 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297366.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118968 | Curators of the CIP | Collection of Institut Pasteur (CIP 109074) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109074 |