Strain identifier

BacDive ID: 133380

Type strain: Yes

Species: Photorhabdus namnaonensis

Strain Designation: PB45.5

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain PB45.5

NCBI tax ID(s): 1851568 (species)

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General

@ref: 66476

BacDive-ID: 133380

DSM-Number: 104082

keywords: genome sequence, Bacteria, Gram-negative, motile, rod-shaped, pigmented

description: Photorhabdus namnaonensis PB45.5 is a Gram-negative, motile, rod-shaped bacterium that has a brown pigmentation and was isolated from entomopathogenic nematodes (Heterorhabdi-; tis baujardi) from Thailand.

NCBI tax id

  • NCBI tax id: 1851568
  • Matching level: species

strain history

@refhistory
66476<- P. Kämpfer, Justus-Liebig-Universität Gießen, Germany; PB45.5
121229CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain PB45.5

doi: 10.13145/bacdive133380.20230509.8.1

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 namnaonensis
  • full scientific name: Photorhabdus namnaonensis (Glaeser et al. 2017) Machado et al. 2018

  • synonyms

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

@ref: 66476

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus namnaonensis

full scientific name: Photorhabdus namnaonensis (Glaeser et al. 2017) Machado et al. 2018

strain designation: PB45.5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25251negative2 µm1 µmrod-shapedyes
121229negativerod-shapedyes

colony morphology

  • @ref: 25251
  • colony size: 2 mm
  • colony color: Slightly yellowish
  • medium used: NA

pigmentation

  • @ref: 25251
  • production: no
  • color: brown
  • name: brown diffusible pigments

multimedia

  • @ref: 66476
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104082.jpg
  • caption: DSM 104082 on medium 535 at 28 °C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25251Nutrient agar (NA)yes
25251brain heart infusion agaryes
25251Trypticase Soy Agar (TSA)yes
25251Reasoner's 2A agar (R2A)yes
25251MacConkeyyes
66476TRYPTICASE 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
66476NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
121229CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
25251positivegrowth10-37
25251nogrowth39-40
66476positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 25251
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25251309162-oxoglutarate-carbon source
25251161933-hydroxybenzoate-carbon source
2525116865gamma-aminobutyric acid-carbon source
25251178794-hydroxybenzoate-carbon source
25251581435-dehydro-D-gluconate-builds acid from
2525117128adipate-carbon source
2525115963ribitol-builds acid from
2525115963ribitol-carbon source
2525118305arbutin-carbon source
2525178208azelaate-carbon source
2525116958beta-alanine-carbon source
2525117968butyrate-carbon source
2525117057cellobiose-builds acid from
2525117057cellobiose-carbon source
2525118333D-arabitol-builds acid from
2525112936D-galactose-carbon source
2525116899D-mannitol-builds acid from
2525116899D-mannitol-carbon source
2525117924D-sorbitol-builds acid from
2525117924D-sorbitol-carbon source
2525165327D-xylose-builds acid from
2525165327D-xylose-carbon source
25251370543-hydroxybutyrate-carbon source
2525117113erythritol-builds acid from
252514853esculin-hydrolysis
252514853esculin-builds acid from
252514853esculin-carbon source
2525128757fructose-builds acid from
2525116813galactitol-builds acid from
2525117859glutaric acid-carbon source
2525117754glycerol-carbon source
2525117754glycerol-builds acid from
2525117268myo-inositol-builds acid from
2525117240itaconate-carbon source
2525130849L-arabinose-builds acid from
2525130849L-arabinose-carbon source
2525118287L-fucose-builds acid from
2525118287L-fucose-carbon source
2525115603L-leucine-carbon source
2525115729L-ornithine-carbon source
2525117295L-phenylalanine-carbon source
2525162345L-rhamnose-builds acid from
2525162345L-rhamnose-carbon source
2525116828L-tryptophan-carbon source
2525117716lactose-builds acid from
2525115792malonate-builds base from
2525168428maltitol-carbon source
2525128053melibiose-builds acid from
2525128053melibiose-carbon source
2525136986mesaconate-carbon source
25251506227N-acetylglucosamine-builds acid from
2525118401phenylacetate-carbon source
2525117272propionate-carbon source
2525117148putrescine-carbon source
2525116634raffinose-builds acid from
2525133942ribose-builds acid from
2525117814salicin-builds acid from
2525117814salicin-carbon source
252519300suberic acid-carbon source
2525117992sucrose-builds acid from
2525117992sucrose-carbon source
2525115708trans-aconitate-carbon source
2525117151xylitol-builds acid from
2525117151xylitol-carbon source
2525116947citrate+builds base from
2525117634D-glucose+builds acid from
2525116024D-mannose+builds acid from
2525115589L-malate+carbon source
2525117306maltose+builds acid from
2525127082trehalose+builds acid from
2525130089acetate+/-carbon source
2525116383cis-aconitate+/-carbon source
2525116947citrate+/-carbon source
2525115824D-fructose+/-carbon source
2525117634D-glucose+/-carbon source
2525116024D-mannose+/-carbon source
2525116988D-ribose+/-carbon source
2525129806fumarate+/-carbon source
2525124265gluconate+/-carbon source
2525117268myo-inositol+/-carbon source
2525116977L-alanine+/-carbon source
2525129991L-aspartate+/-carbon source
2525117203L-proline+/-carbon source
2525117115L-serine+/-carbon source
2525124996lactate+/-carbon source
2525117306maltose+/-carbon source
2525128037N-acetylgalactosamine+/-carbon source
25251506227N-acetylglucosamine+/-carbon source
2525115361pyruvate+/-carbon source
2525127082trehalose+/-carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2525115688acetoinno
2525116136hydrogen sulfideno
2525135581indoleno

metabolite tests

  • @ref: 25251
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
25251arginine dihydrolase-3.5.3.6
25251beta-galactosidase-3.2.1.23
25251catalase-1.11.1.6
25251cytochrome oxidase-1.9.3.1
25251DNase+
25251gelatinase+
25251lysine decarboxylase-4.1.1.18
25251ornithine decarboxylase-4.1.1.17
25251urease-3.5.1.5
68369cytochrome oxidase-1.9.3.1
68369gelatinase+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
66476--+++++-+-+++++--++--
66476-+----+-+-++++-+/--++--
66476--+++++-+-+++++--++--
66476-+----+-+-++++---++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
25251entomopathogenic nematodes (Heterorhabdi- tis baujardi) from ThailandNam Nao district of Phetchabun in central ThailandThailandTHAAsia161012009-10
121229H. BaujardiNam Nao, Sub District, Nam Nao District, PhetchabunThailandTHAAsia2009-01-02

isolation source categories

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

Safety information

risk assessment

  • @ref: 121229
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Photorhabdus namnaonensis PB45.5
  • accession: GCA_001684335
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1851568

GC content

@refGC-contentmethod
2525142.5
6647642.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes60.856no
gram-positiveno98.402yes
anaerobicno98.206no
aerobicyes86.148no
halophileno86.652no
spore-formingno93.838no
thermophileno98.827no
glucose-utilyes92.506yes
motileyes87.783yes
glucose-fermentyes84.668no

External links

@ref: 66476

culture collection no.: LMG 29915, CCM 8729, DSM 104082, CIP 111196

straininfo link

  • @ref: 91420
  • straininfo: 404126

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
25251S. P. T. Glaeser, N. J.,Thanwisai, A.,Chantratita, N.,Bode, H. B.,Kämpfer, P.Photorhabdus luminescens subsp. namnaonensis subsp. nov., isolated from Heterorhabditis baujardi nematodes10.1099/ijsem.0.001761IJSEM 67: 1046-1051 201728032540
66476Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104082Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104082)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
91420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404126.1
121229Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111196Collection of Institut Pasteur (CIP 111196)