Strain identifier

BacDive ID: 5049

Type strain: Yes

Species: Photorhabdus caribbeanensis

Strain Designation: HG29

Strain history: CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain HG29

NCBI tax ID(s): 1004165 (species)

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General

@ref: 16255

BacDive-ID: 5049

DSM-Number: 22391

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, animal pathogen

description: Photorhabdus caribbeanensis HG29 is an obligate aerobe, mesophilic, motile animal pathogen that was isolated from nematode Heterorhabditis bacteriophora.

NCBI tax id

  • NCBI tax id: 1004165
  • Matching level: species

strain history

@refhistory
16255<- P. Tailliez, INRA, Univ. Montpellier, France; HG29 <- N. E. Boemare <- M. Fischer-Le Saux
117181CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain HG29

doi: 10.13145/bacdive5049.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Photorhabdus
  • species: Photorhabdus caribbeanensis
  • full scientific name: Photorhabdus caribbeanensis (Tailliez et al. 2010) Machado et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Photorhabdus luminescens subsp. caribbeanensis

@ref: 16255

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus caribbeanensis

full scientific name: Photorhabdus caribbeanensis (Tailliez et al. 2010) Machado et al. 2018

strain designation: HG29

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.869
6948099.935negative
117181nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16255NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37891MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
16255TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
117181CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16255positivegrowth28mesophilic
37891positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117181
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no98.993

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11718117632nitrate-reduction
11718116301nitrite-reduction

metabolite production

  • @ref: 117181
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
117181oxidase-
117181catalase+1.11.1.6
117181urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117181-+-+-++-+-+++----+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
16255nematode Heterorhabditis bacteriophoraHeterorhabditis bacteriophoraCaribbean islandsGuadeloupeFRAMiddle and South America
117181Animal, Nematode, Heterorhabditis bacteriophoraGuadeloupeFranceFRAEurope1999

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_15787.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1857;98_2282;99_15787&stattab=map
  • Last taxonomy: Photorhabdus caribbeanensis
  • 16S sequence: EU930345
  • Sequence Identity:
  • Total samples: 8
  • animal counts: 8

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16255yes1Risk group (German classification)
1171811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16255
  • description: Photorhabdus luminescens strain HG29 16S ribosomal RNA gene, partial sequence
  • accession: EU930345
  • length: 1379
  • database: ena
  • NCBI tax ID: 1004165

Genome sequences

  • @ref: 66792
  • description: Photorhabdus caribbeanensis HG29
  • accession: GCA_018448885
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1004165

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.325no
flagellatedyes58.985no
gram-positiveno98.658no
anaerobicno97.737no
aerobicyes82.595no
halophileno87.788no
spore-formingno94.519no
thermophileno98.392yes
glucose-utilyes93.561no
glucose-fermentyes84.774no

External links

@ref: 16255

culture collection no.: DSM 22391, CIP 109949

straininfo link

  • @ref: 74544
  • straininfo: 370405

Reference

@idauthorscataloguedoi/urltitle
16255Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22391)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22391
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
37891Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7750
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74544Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370405.1StrainInfo: A central database for resolving microbial strain identifiers
117181Curators of the CIPCollection of Institut Pasteur (CIP 109949)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109949