Strain identifier

BacDive ID: 5036

Type strain: Yes

Species: Photorhabdus laumondii

Strain Designation: TT01, HT1

Strain history: CIP <- 1998, N. Boemare, Univ. Montpellier II, Lab. Pathol. comparée, Montpellier, France: strain TT01

NCBI tax ID(s): 2218628 (species)

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General

@ref: 5632

BacDive-ID: 5036

DSM-Number: 15139

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, animal pathogen

description: Photorhabdus laumondii TT01 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from nematode Heterorhabditis bacteriophora.

NCBI tax id

  • NCBI tax id: 2218628
  • Matching level: species

strain history

@refhistory
5632<- CIP <- N. Boemare, Univ. Montpellier; TT01
397441998, N. Boemare, Univ. Montpellier II, Lab. Pathol. comParée, Montpellier, France: strain TT01
120572CIP <- 1998, N. Boemare, Univ. Montpellier II, Lab. Pathol. comparée, Montpellier, France: strain TT01

doi: 10.13145/bacdive5036.20230509.8.1

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 laumondii
  • full scientific name: Photorhabdus laumondii (Fischer-Le Saux et al. 1999) Machado et al. 2018

  • synonyms

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

@ref: 5632

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus laumondii

full scientific name: Photorhabdus laumondii (Fischer-Le Saux et al. 1999) Machado et al. 2018

strain designation: TT01, HT1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.89
6948099.942negative
120572nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5632REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a; 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
5632REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
39744MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120572CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5632positivegrowth28mesophilic
39744positivegrowth30mesophilic
120572positivegrowth30mesophilic
120572nogrowth5psychrophilic
120572nogrowth10psychrophilic
120572nogrowth37mesophilic
120572nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120572
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no98.946

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
6836917634D-glucose-fermentation
6836917632nitrate-reduction
12057229864mannitol-fermentation
12057216947citrate+carbon source
12057217234glucose+fermentation
12057217716lactose-fermentation
12057217632nitrate-reduction
12057216301nitrite-reduction
12057215792malonate-assimilation
120572132112sodium thiosulfate-builds gas from
12057217234glucose+degradation

antibiotic resistance

  • @ref: 120572
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120572
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12057215688acetoin-
12057217234glucose-

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+
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
120572oxidase-
120572beta-galactosidase-3.2.1.23
120572alcohol dehydrogenase-1.1.1.1
120572gelatinase+/-
120572amylase-
120572DNase-
120572caseinase+3.4.21.50
120572catalase+1.11.1.6
120572tween esterase+
120572lecithinase-
120572lipase-
120572lysine decarboxylase-4.1.1.18
120572ornithine decarboxylase-4.1.1.17
120572phenylalanine ammonia-lyase-4.3.1.24
120572protease+
120572tryptophan deaminase-
120572urease+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
120572-+++-+----++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5632-+-++++++-+-+++---+--
5632----+++-+-+-+++------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120572++--+----++--------+-----------++----------------++--++----++-----------------+++-----+---+--++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5632nematode Heterorhabditis bacteriophoraHeterorhabditis bacteriophoraTrinidadTrinidad and TobagoTTOMiddle and South America
120572Animal, Nematode Heterorhabditis bacteriophora (group HP88)Trinidad and TobagoTTONorth America1996

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4565.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1857;98_2282;99_4565&stattab=map
  • Last taxonomy: Photorhabdus laumondii
  • 16S sequence: AJ007404
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 1
  • aquatic counts: 16
  • animal counts: 23
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5632yes1Risk group (German classification)
1205721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photorhabdus luminescens subsp. laumondii gene for 16S rRNA, partial sequence, strain: TT01AB3558741499ena141679
20218Photorhabdus luminescens subsp. laumondii partial 16S rRNA gene, strain TT01AJ0074041540ena141679
20218Photorhabdus luminescens subsp. laumondii strain TT01 16S ribosomal RNA gene, partial sequenceAY2786461499ena141679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus laumondii subsp. laumondii TT01GCA_003343245completencbi141679
66792Photorhabdus laumondii subsp. laumondii strain TT01141679.8completepatric141679

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.156no
flagellatedyes65.196no
gram-positiveno98.373no
anaerobicno98.204no
aerobicyes86.894no
halophileno88.64no
spore-formingno93.932no
glucose-utilyes93.253no
thermophileno98.213yes
glucose-fermentyes84.692yes

External links

@ref: 5632

culture collection no.: DSM 15139, CCM 7076, CIP 105565

straininfo link

  • @ref: 74531
  • straininfo: 69652

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5632Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15139)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15139
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
39744Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17598
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
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
74531Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID69652.1StrainInfo: A central database for resolving microbial strain identifiers
120572Curators of the CIPCollection of Institut Pasteur (CIP 105565)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105565