Strain identifier

BacDive ID: 5030

Type strain: No

Species: Photorhabdus luminescens

Strain Designation: LN2

Strain history: <- R.-U. Ehlers; LN2

NCBI tax ID(s): 29488 (species)

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General

@ref: 4639

BacDive-ID: 5030

DSM-Number: 12191

keywords: genome sequence, Bacteria, mesophilic, animal pathogen

description: Photorhabdus luminescens LN2 is a mesophilic animal pathogen that was isolated from nematode Heterorhabditis indica.

NCBI tax id

  • NCBI tax id: 29488
  • Matching level: species

strain history

  • @ref: 4639
  • history: <- R.-U. Ehlers; LN2

doi: 10.13145/bacdive5030.20230509.8.1

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 luminescens
  • full scientific name: Photorhabdus luminescens (Thomas and Poinar 1979) Boemare et al. 1993

  • synonyms

    • @ref: 20215
    • synonym: Xenorhabdus luminescens

@ref: 4639

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus luminescens

full scientific name: Photorhabdus luminescens (Thomas and Poinar 1979) Boemare et al. 1993 emend. Fischer-Le Saux et al. 1999 emend. Machado et al. 2018 emend. Machado et al. 2019

strain designation: LN2

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4639REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
4639REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: 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

culture temp

  • @ref: 4639
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan+energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4639-+-++++++-++++++-++--

Isolation, sampling and environmental information

isolation

  • @ref: 4639
  • sample type: nematode Heterorhabditis indica
  • host species: Heterorhabditis indica
  • geographic location: Coimbatora, Tamil Nadu
  • country: India
  • origin.country: IND
  • continent: Asia

isolation source categories

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

Safety information

risk assessment

  • @ref: 4639
  • pathogenicity animal: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus luminescens LN2GCA_000767775scaffoldncbi29488
66792Photorhabdus luminescens LN229488.3wgspatric29488
66792Photorhabdus luminescens LN22630968405draftimg29488

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.928no
flagellatedyes65.703no
gram-positiveno98.559no
anaerobicno98.011no
aerobicyes80.422no
halophileno88.559no
spore-formingno93.722no
thermophileno98.621no
glucose-utilyes93.201yes
glucose-fermentyes85.193yes

External links

@ref: 4639

culture collection no.: DSM 12191

straininfo link

  • @ref: 74525
  • straininfo: 49251

literature

  • topic: Phylogeny
  • Pubmed-ID: 9924819
  • title: Molecular identification of Photorhabdus luminescens strains by amplification of specific fragments of the 16S ribosomal DNA.
  • authors: Ehlers RU, Niemann I
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/S0723-2020(98)80063-5
  • year: 1998
  • mesh: Animals, DNA Primers, Enterobacteriaceae/*classification/*genetics, Polymerase Chain Reaction/*methods, RNA, Bacterial/*analysis, RNA, Ribosomal, 16S/*analysis, Rhabditoidea/*microbiology, Symbiosis/physiology

Reference

@idauthorscataloguedoi/urltitle
4639Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12191)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12191
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
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)
68369Automatically annotated from API 20NE
74525Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49251.1StrainInfo: A central database for resolving microbial strain identifiers