Strain identifier

BacDive ID: 5032

Type strain: Yes

Species: Photorhabdus luminescens

Strain Designation: Hb

Strain history: CIP <- 2000, N. Boemare, Montpellier Univ., Montpellier, France <- 1984, CSIRO <- 1980, ATCC <- G.M. Thomas: strain Hb, Xenorhabdus luminescens

NCBI tax ID(s): 29488 (species)

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General

@ref: 1361

BacDive-ID: 5032

DSM-Number: 3368

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, animal pathogen

description: Photorhabdus luminescens Hb is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from Nematode Heterorhabditis bacteriophora.

NCBI tax id

  • NCBI tax id: 29488
  • Matching level: species

strain history

@refhistory
1361<- E. Stackebrandt <- ATCC <- G.M. Thomas; Hb
120673CIP <- 2000, N. Boemare, Montpellier Univ., Montpellier, France <- 1984, CSIRO <- 1980, ATCC <- G.M. Thomas: strain Hb, Xenorhabdus luminescens

doi: 10.13145/bacdive5032.20230509.8.1

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: 1361

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: Hb

type strain: yes

Morphology

cell morphology

  • @ref: 120673
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1361TRYPTICASE 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
1361NUTRIENT 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
40311Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120673CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1361positivegrowth30mesophilic
40311positivegrowth30mesophilic
120673positivegrowth30-37mesophilic
120673nogrowth5psychrophilic
120673nogrowth10psychrophilic
120673nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120673
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369nitrate-reduction17632
120673mannitol-fermentation29864
120673citrate+carbon source16947
120673esculin-hydrolysis4853
120673glucose+fermentation17234
120673lactose-fermentation17716
120673nitrate-reduction17632
120673nitrite-reduction16301
120673malonate-assimilation15792
120673sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 120673
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120673
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12067315688acetoin-
12067317234glucose-

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
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120673oxidase-
120673beta-galactosidase-3.2.1.23
120673alcohol dehydrogenase-1.1.1.1
120673gelatinase+/-
120673amylase-
120673DNase-
120673caseinase+3.4.21.50
120673catalase+1.11.1.6
120673tween esterase-
120673lecithinase-
120673lipase+
120673lysine decarboxylase-4.1.1.18
120673ornithine decarboxylase-4.1.1.17
120673phenylalanine ammonia-lyase-4.3.1.24
120673protease+
120673tryptophan deaminase-
120673urease-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
120673-+---++-+-+----+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1361-++--++-+-+++++--++--
1361------+-+-+++++--++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120673+---+-----+++---++---+--+--+---+-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120673++-++----++--------+----+------+++---------------++--++----++-+--+------------+++-----+--++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
1361Nematode Heterorhabditis bacteriophoraHeterorhabditis bacteriophoraBreaconAustraliaAUSAustralia and Oceania
120673Animal, Nematode, Heterorhabditis bacteriophoraAustraliaAUSAustralia and Oceania1978

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2472.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1261;98_1516;99_2472&stattab=map
  • Last taxonomy: Photorhabdus luminescens
  • 16S sequence: X82248
  • Sequence Identity:
  • Total samples: 39
  • soil counts: 1
  • aquatic counts: 13
  • animal counts: 24
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1361yes1Risk group (German classification)
1206731Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photorhabdus luminescens subsp. luminescens strain ATCC 29999 16S ribosomal RNA gene, partial sequenceAY8706581475ena171439
20218Photorhabdus luminescens gene for 16S rRNA, partial sequence, strain: ATCC 29999D780051482ena29488
20218Photorhabdus luminescens subsp. luminescens 16S rRNA gene, strain (DSM 3368)X822481499ena171439
20218Photorhabdus luminescens subsp. luminescens strain Hb 16S ribosomal RNA gene, partial sequenceAY2786401499ena171439

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus luminescens subsp. luminescens DSM 3368GCA_001083805contigncbi171439
66792Photorhabdus luminescens ATCC 29999GCA_900102985scaffoldncbi29488
66792Photorhabdus luminescens strain ATCC 2999929488.49wgspatric29488
66792Photorhabdus luminescens subsp. luminescens strain DSM 3368171439.3wgspatric171439
66792Photorhabdus luminescens luminescens DSM 33682648501375draftimg171439
66792Photorhabdus luminescens luminescens ATCC 299992597490348draftimg1354241

GC content

  • @ref: 1361
  • GC-content: 44.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.208no
flagellatedyes59.006no
gram-positiveno98.476no
anaerobicno98.409no
aerobicyes83.206no
halophileno87.583no
spore-formingno93.947no
glucose-fermentyes84.565no
thermophileno98.182yes
glucose-utilyes93.271yes

External links

@ref: 1361

culture collection no.: DSM 3368, ATCC 29999, CCM 7077, CIP 106429, NCIMB 12670

straininfo link

  • @ref: 74527
  • straininfo: 11108

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8206831Identification of the genes encoding NAD(P)H-flavin oxidoreductases that are similar in sequence to Escherichia coli Fre in four species of luminous bacteria: Photorhabdus luminescens, Vibrio fischeri, Vibrio harveyi, and Vibrio orientalis.Zenno S, Saigo KJ Bacteriol10.1128/jb.176.12.3544-3551.19941994Amino Acid Sequence, Bacteria/enzymology/*genetics, Bacterial Proteins/genetics/metabolism, Base Sequence, FMN Reductase, Genes, Bacterial/*genetics, Genomic Library, *Luminescent Measurements, Molecular Sequence Data, NADH, NADPH Oxidoreductases/*genetics, NADP/metabolism, Oxidation-Reduction, *Oxidoreductases, Riboflavin/metabolism, Sequence Homology, Species Specificity, Vibrio/enzymology/*geneticsMetabolism
Pathogenicity10408101Survival of insect pathogenic and human clinical isolates of Photorhabdus luminescens in previously sterile soil.Bleakley BH, Chen XCan J Microbiol10.1139/w98-2311999Amino Acids, Animals, Calcium Carbonate, Colony Count, Microbial, Enterobacteriaceae/*growth & development, Gelatin, Humans, Nematoda/microbiology, *Soil Microbiology, Time Factors
Phylogeny10555346Polyphasic classification of the genus Photorhabdus and proposal of new taxa: P. luminescens subsp. luminescens subsp. nov., P. luminescens subsp. akhurstii subsp. nov., P. luminescens subsp. laumondii subsp. nov., P. temperata sp. nov., P. temperata subsp. temperata subsp. nov. and P. asymbiotica sp. nov.Fischer-Le Saux M, Viallard V, Brunel B, Normand P, Boemare NEInt J Syst Bacteriol10.1099/00207713-49-4-16451999Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Photorhabdus/*classification/genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny30688647Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes.Machado RAR, Bruno P, Arce CCM, Liechti N, Kohler A, Bernal J, Bruggmann R, Turlings TCJInt J Syst Evol Microbiol10.1099/ijsem.0.0031542019Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Mexico, Nucleic Acid Hybridization, Photorhabdus/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditoidea/*microbiology, Sequence Analysis, DNA, SoilTranscriptome
Enzymology33411135Identification and Characterization of an Efficient Phenylalanine Ammonia-Lyase from Photorhabdus luminescens.Zhang F, Ren J, Zhan JAppl Biochem Biotechnol10.1007/s12010-020-03477-62021*Bacterial Proteins/chemistry/genetics, *Phenylalanine Ammonia-Lyase/chemistry/genetics, *Photorhabdus/enzymology/genetics, Recombinant Proteins/chemistry/genetics
33791681The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria.Pan J, Williams E, Sung W, Lynch M, Long HMar Life Sci Technol10.1007/s42995-020-00060-02020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1361Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3368)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3368
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40311Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18559
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
68371Automatically annotated from API 50CH acid
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
74527Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11108.1StrainInfo: A central database for resolving microbial strain identifiers
120673Curators of the CIPCollection of Institut Pasteur (CIP 106429)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106429