Strain identifier

BacDive ID: 158410

Type strain: Yes

Species: Photorhabdus bodei

Strain Designation: LJ24-63

Strain history: <- R. Machado, Univ. Bern, Switzerland; LJ24-63 <-

NCBI tax ID(s): 2029681 (species)

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General

@ref: 65086

BacDive-ID: 158410

DSM-Number: 105690

keywords: genome sequence, 16S sequence, Bacteria, motile

description: Photorhabdus bodei LJ24-63 is a motile bacterium that was isolated from entomopathogenic nematodes.

NCBI tax id

  • NCBI tax id: 2029681
  • Matching level: species

strain history

  • @ref: 65086
  • history: <- R. Machado, Univ. Bern, Switzerland; LJ24-63 <-

doi: 10.13145/bacdive158410.20230509.8.1

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 bodei
  • full scientific name: Photorhabdus bodei Machado et al. 2018

@ref: 65086

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus bodei

full scientific name: Photorhabdus bodei Machado et al. 2018

strain designation: LJ24-63

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.571
6948099.946negative

colony morphology

  • @ref: 66582
  • colony color: orangey or yellowish
  • medium used: Nutrient agar (NA)

multimedia

  • @ref: 65086
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105690.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65086TRYPTICASE 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
66582Nutrient agar (NA)yes

culture temp

  • @ref: 66582
  • growth: positive
  • type: growth
  • temperature: 12-37

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no99.108
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
665826731melezitose-builds acid from
6658212936D-galactose-builds acid from
6658215443inulin-builds acid from
6658215963ribitol-builds acid from
6658216443D-tagatose-builds acid from
6658216634raffinose-builds acid from
6658216813galactitol-builds acid from
6658216899D-mannitol-builds acid from
6658217057cellobiose-builds acid from
6658217108D-arabinose-builds acid from
6658217113erythritol-builds acid from
6658217151xylitol-builds acid from
6658217266L-sorbose-builds acid from
6658217716lactose-builds acid from
6658217924D-sorbitol-builds acid from
6658217992sucrose-builds acid from
6658218287L-fucose-builds acid from
6658218305arbutin-builds acid from
6658218333D-arabitol-builds acid from
6658218403L-arabitol-builds acid from
6658227613amygdalin-builds acid from
6658228017starch-builds acid from
6658228053melibiose-builds acid from
6658228066gentiobiose-builds acid from
6658228087glycogen-builds acid from
6658228847D-fucose-builds acid from
6658230849L-arabinose-builds acid from
6658232032potassium gluconate-builds acid from
6658232528turanose-builds acid from
6658243943methyl alpha-D-mannoside-builds acid from
6658262318D-lyxose-builds acid from
6658262345L-rhamnose-builds acid from
6658265327D-xylose-builds acid from
6658265328L-xylose-builds acid from
6658274863methyl beta-D-xylopyranoside-builds acid from
66582320061methyl alpha-D-glucopyranoside-builds acid from
66582potassium 2-dehydro-D-gluconate-builds acid from
66582potassium 5-dehydro-D-gluconate-builds acid from
6658215824D-fructose+builds acid from
6658216024D-mannose+builds acid from
6658216551D-trehalose+builds acid from
6658216988D-ribose+builds acid from
6658217268myo-inositol+builds acid from
6658217306maltose+builds acid from
6658217634D-glucose+builds acid from
6658217754glycerol+builds acid from
6658217814salicin+builds acid from
6658259640N-acetylglucosamine+builds acid from
66582esculin ferric citrate+builds acid from
6658217268myo-inositol-oxidation
6658217992sucrose-oxidation
6658222599arabinose-oxidation
6658226546rhamnose-oxidation
6658227613amygdalin-oxidation
6658228053melibiose-oxidation
6658229864mannitol-oxidation
6658230911sorbitol-oxidation
6658217234glucose+oxidation
6658217632nitrate-reduction
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

@refChebi-IDmetaboliteproduction
6658235581indoleyes
6658215688acetoinno
6658216136hydrogen sulfideno
6836935581indoleyes

metabolite tests

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

enzymes

@refvalueactivityec
66582arginine dihydrolase-3.5.3.6
66582beta-galactosidase-3.2.1.23
66582cytochrome oxidase-1.9.3.1
66582lysine decarboxylase-4.1.1.18
66582ornithine decarboxylase-4.1.1.17
66582urease-3.5.1.5
66582catalase+1.11.1.6
66582gelatinase+
66582tryptophan deaminase+4.1.99.1
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
65086-++-+++-+-+-+++--++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
65086entomopathogenic nematodesLiaoning, JinzhouChinaCHNAsia
66582Heterorhabditis beicherrianaLiaoning ProvinceChinaCHNAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66582
  • description: Photorhabdus bodei strain LJ24-63 16S ribosomal RNA gene, partial sequence
  • accession: MK039080
  • length: 1349
  • database: ena
  • NCBI tax ID: 2029681

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus bodei LJ24-63GCA_003287735scaffoldncbi2029681
66792Photorhabdus bodei LJ24-632840807575draftimg2029681

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.714no
flagellatedyes57.457no
gram-positiveno98.376no
anaerobicno97.938no
aerobicyes87.135no
halophileno89.278no
spore-formingno93.326no
glucose-utilyes94.14yes
thermophileno98.062no
glucose-fermentyes86.613yes

External links

@ref: 65086

culture collection no.: DSM 105690, CCOS 1159

straininfo link

  • @ref: 111213
  • straininfo: 400626

literature

  • topic: Phylogeny
  • Pubmed-ID: 29877789
  • title: Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov.
  • authors: Machado RAR, Wuthrich D, Kuhnert P, Arce CCM, Thonen L, Ruiz C, Zhang X, Robert CAM, Karimi J, Kamali S, Ma J, Bruggmann R, Erb M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002820
  • year: 2018
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Genome, Bacterial, Nucleic Acid Hybridization, Photorhabdus/*classification/genetics, *Phylogeny, Rhabditoidea/*microbiology, Sequence Analysis, DNA, Symbiosis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
65086Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105690Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105690)
66582Ricardo A. R. Machado, Daniel Wüthrich, Peter Kuhnert, Carla C. M. Arce, Lisa Thönen, Celia Ruiz, Xi Zhang, Christelle A. M. Robert, Javad Karimi, Shokoofeh Kamali, Juan Ma, Rémy Bruggmann and Matthias ErbWhole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov.10.1099/ijsem.0.002820IJSEM 68: 2664-2681 201829877789
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111213Reimer, 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-ID400626.1