Strain identifier
BacDive ID: 5185
Type strain:
Species: Xenorhabdus nematophila
Strain history: CIP <- 2005, CCUG <- 1983, F. Gavini, INSERM, Villeneuve d'Ascq, France <- G.O. Poinar, Jr <- G. M. Thomas
NCBI tax ID(s): 406817 (strain), 628 (species)
General
@ref: 1363
BacDive-ID: 5185
DSM-Number: 3370
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, animal pathogen
description: Xenorhabdus nematophila DSM 3370 is an aerobe, mesophilic, motile animal pathogen that was isolated from intestinal lumen of Neoplectana sp..
NCBI tax id
NCBI tax id | Matching level |
---|---|
628 | species |
406817 | strain |
strain history
@ref | history |
---|---|
1363 | <- E. Stackebrandt <- ATCC <- G.O. Poinar, Jr. and G.M.Thomas ("Achromobacter nematophilus") |
121262 | CIP <- 2005, CCUG <- 1983, F. Gavini, INSERM, Villeneuve d'Ascq, France <- G.O. Poinar, Jr <- G. M. Thomas |
doi: 10.13145/bacdive5185.20230509.8.1
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 nematophila
- full scientific name: Xenorhabdus nematophila corrig. (Poinar and Thomas 1965) Thomas and Poinar 1979 (Approved Lists 1980)
synonyms
@ref synonym 20215 Xenorhabdus nematophilus 20215 Achromobacter nematophilus
@ref: 1363
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Morganellaceae
genus: Xenorhabdus
species: Xenorhabdus nematophila
full scientific name: Xenorhabdus nematophila (Poinar and Thomas 1965) Thomas and Poinar 1979
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.526 | ||
69480 | 99.874 | negative | ||
121262 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1363 | REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) | yes | https://mediadive.dsmz.de/medium/535b | Name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water |
121262 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1363 | positive | growth | 26 | mesophilic |
46042 | positive | growth | 30 | mesophilic |
46042 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
46042 | aerobe |
46042 | microaerophile |
121262 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.553 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
121262 | 17632 | nitrate | - | reduction |
121262 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121262 | 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 | gelatinase | + | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121262 | oxidase | - | |
121262 | alcohol dehydrogenase | - | 1.1.1.1 |
121262 | catalase | - | 1.11.1.6 |
121262 | lysine decarboxylase | - | 4.1.1.18 |
121262 | ornithine decarboxylase | - | 4.1.1.17 |
121262 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121262 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | - | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1363 | - | - | + | - | - | - | + | - | + | - | + | - | + | - | - | - | - | - | - | - | - |
1363 | - | - | - | - | - | - | + | - | + | - | + | - | + | - | - | - | - | + | - | + | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | isolation date |
---|---|---|---|
1363 | intestinal lumen of Neoplectana sp. | Neoplectana | |
46042 | Intestinal lumen of Neoaplectana sp. | ||
121262 | Intestinal lumen DD 136 strain of Neoaplectana carpocapsae Weiser | 1964 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Invertebrates (Other) | #Nematoda |
#Host Body-Site | #Gastrointestinal tract |
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
1363 | yes | 1 | Risk group (German classification) |
121262 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Xenorhabdus nematophila gene for 16S rRNA, partial sequence, strain: ATCC 19061 | D78009 | 1479 | ena | 628 |
20218 | Xenorhabdus nematophila 16S ribosomal RNA gene, partial sequence | AY278674 | 1496 | ena | 628 |
20218 | X.nematophilus 16S rRNA gene (DSM 3370) | X82251 | 1497 | ena | 628 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xenorhabdus nematophila ATCC 19061 | GCA_000252955 | chromosome | ncbi | 406817 |
66792 | Xenorhabdus nematophila ATCC 19061 | 406817.27 | complete | patric | 406817 |
66792 | Xenorhabdus nematophila ATCC 19061 | 406817.32 | plasmid | patric | 406817 |
66792 | Xenorhabdus nematophila ATCC 19061 | 649633108 | complete | img | 406817 |
GC content
- @ref: 1363
- GC-content: 43.4
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.139 | no |
anaerobic | no | 97.357 | yes |
halophile | no | 89.67 | no |
spore-forming | no | 92.143 | no |
glucose-util | yes | 90.418 | yes |
aerobic | yes | 76.116 | no |
flagellated | yes | 55.778 | no |
motile | yes | 87.909 | no |
thermophile | no | 98.167 | no |
glucose-ferment | yes | 84.799 | no |
External links
@ref: 1363
culture collection no.: DSM 3370, ATCC 19061, CCM 7081, CCUG 14189, CIP 108994, LMG 1036, CUETM 8319
straininfo link
- @ref: 74677
- straininfo: 6427
literature
Pubmed-ID | title | authors | journal | DOI | year | topic | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
16348462 | Characterization of Tn5-Induced Mutants of Xenorhabdus nematophilus ATCC 19061. | Xu J, Olson ME, Kahn ML, Hurlbert RE | Appl Environ Microbiol | 10.1128/aem.57.4.1173-1180.1991 | 1991 | |||
22125637 | The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. | Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Leon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Medigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H | PLoS One | 10.1371/journal.pone.0027909 | 2011 | Phylogeny | Animals, Chromosomes, Bacterial/genetics, DNA, Bacterial/chemistry/genetics, Enterobacteriaceae/classification/genetics/physiology, *Genetic Variation, Genome, Bacterial/*genetics, Genomics/methods, Host-Parasite Interactions, Host-Pathogen Interactions, Insecta/microbiology/parasitology, Molecular Sequence Data, Nematoda/microbiology/physiology, Photorhabdus/classification/*genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Symbiosis, Xenorhabdus/classification/*genetics/physiology | Genetics |
30114602 | TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila. | Yadav M, Rathore JS | Comput Biol Chem | 10.1016/j.compbiolchem.2018.07.010 | 2018 | Genetics | Bacterial Proteins/*genetics, Bacterial Toxins/*genetics, Genomics, Photorhabdus/genetics, Phylogeny, Toxin-Antitoxin Systems/*genetics, Xenorhabdus/*genetics | Phylogeny |
30919769 | Characteristics and Function of the Chitin Binding Protein from Xenorhabdus nematophila. | Liu J, Song P, Zhang J, Nangong Z, Liu X, Gao Y, Wang Q | Protein Pept Lett | 10.2174/0929866526666190327143335 | 2019 | Pathogenicity | Animals, Antifungal Agents/*chemistry/pharmacology, Ascomycota/drug effects, Bacterial Proteins/*chemistry/genetics/pharmacology, Carrier Proteins/*chemistry/genetics/pharmacology, Chitin/*chemistry, Escherichia coli/genetics, Insecticides/chemistry, Larva/drug effects, Moths/drug effects, Protein Binding, Xenorhabdus/*chemistry | |
32422264 | Novel insecticidal chitinase from the insect pathogen Xenorhabdus nematophila. | Mahmood S, Kumar M, Kumari P, Mahapatro GK, Banerjee N, Sarin NB | Int J Biol Macromol | 10.1016/j.ijbiomac.2020.05.078 | 2020 | Enzymology | Chemical Phenomena, Chitinases/*chemistry/genetics/isolation & purification/*pharmacology, Circular Dichroism, Cloning, Molecular, Dose-Response Relationship, Drug, Gene Expression, Insecticides/*chemistry/*pharmacology, Models, Biological, Protein Conformation, Recombinant Proteins, Sequence Analysis, DNA, Spectrum Analysis, Xenorhabdus/*enzymology/genetics | Transcriptome |
34839000 | Functional and transcriptional analysis of chromosomal encoded hipBA(Xn2) type II toxin-antitoxin (TA) module from Xenorhabdus nematophila. | Yadav M, Rathore JS | Microb Pathog | 10.1016/j.micpath.2021.105309 | 2021 | Pathogenicity | *Antitoxins/genetics, Bacterial Proteins/genetics, DNA-Binding Proteins, Escherichia coli/genetics, *Escherichia coli Proteins, *Toxin-Antitoxin Systems/genetics, *Xenorhabdus/genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1363 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3370) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3370 | |||
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 | |
46042 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 14189) | https://www.ccug.se/strain?id=14189 | |||
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 | |
68369 | Automatically annotated from API 20NE | |||||
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 | |||
74677 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID6427.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121262 | Curators of the CIP | Collection of Institut Pasteur (CIP 108994) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108994 |