Strain identifier

BacDive ID: 5044

Type strain: Yes

Species: Photorhabdus thracensis

Strain Designation: 39-8

Strain history: CIP <- 2004 NCIMB <- S. Hazir, Turkey: strain 39-8

NCBI tax ID(s): 230089 (species)

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General

@ref: 5752

BacDive-ID: 5044

DSM-Number: 15199

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, animal pathogen

description: Photorhabdus thracensis 39-8 is an obligate aerobe, mesophilic, motile animal pathogen that was isolated from entomopathogenic nematodes .

NCBI tax id

  • NCBI tax id: 230089
  • Matching level: species

strain history

@refhistory
5752<- S. Hazir; 39-8
123534CIP <- 2004 NCIMB <- S. Hazir, Turkey: strain 39-8

doi: 10.13145/bacdive5044.20230509.8.1

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 thracensis
  • full scientific name: Photorhabdus thracensis (Hazir et al. 2004) Machado et al. 2018

  • synonyms

    @refsynonym
    20215Photorhabdus temperata subsp. thracensis
    20215Photorhabdus luminescens subsp. thracensis

@ref: 5752

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus thracensis

full scientific name: Photorhabdus thracensis (Hazir et al. 2004) Machado et al. 2018

strain designation: 39-8

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.939
6948099.965negative
123534negativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5752TRYPTICASE 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
33988MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123534CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5752positivegrowth30mesophilic
33988positivegrowth30mesophilic
123534positivegrowth30-37mesophilic
123534nogrowth5psychrophilic
123534nogrowth10psychrophilic
123534nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123534
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.615

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
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-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
123534mannitol-fermentation29864
123534citrate-carbon source16947
123534esculin+hydrolysis4853
123534glucose+fermentation17234
123534lactose-fermentation17716
123534nitrate-reduction17632
123534nitrite-reduction16301
123534malonate-assimilation15792
123534sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 123534
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123534
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12353415688acetoin-
12353417234glucose-

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
123534oxidase-
123534beta-galactosidase-3.2.1.23
123534alcohol dehydrogenase-1.1.1.1
123534gelatinase+
123534amylase-
123534DNase-
123534caseinase+3.4.21.50
123534catalase+1.11.1.6
123534tween esterase-
123534lecithinase-
123534lipase-
123534lysine decarboxylase-4.1.1.18
123534ornithine decarboxylase-4.1.1.17
123534phenylalanine ammonia-lyase-4.3.1.24
123534protease+
123534tryptophan deaminase-
123534urease-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
123534-+++-++-+-+------+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123534----------++/-+--------+-+---+/----------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123534+--++----++-------++-----------++----------+-----+------+--++--+-----------+---++-----+---+++++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
5752entomopathogenic nematodes (Heterorhabditis bacteriophora)Heterorhabditis bacteriophoraTurkeyTUR
123534Animal, Intestine of the entomopathogenic nematode Heterorhabditis bacteriophoraTurkeyTURAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4681.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1857;98_3510;99_4681&stattab=map
  • Last taxonomy: Photorhabdus thracensis subclade
  • 16S sequence: AJ560634
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 1
  • aquatic counts: 2
  • animal counts: 39
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5752yes1Risk group (German classification)
1235341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5752
  • description: Photorhabdus luminescens subsp. thraceaensis 16S rRNA gene, type strain DSM 15199T
  • accession: AJ560634
  • length: 1516
  • database: ena
  • NCBI tax ID: 230089

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus thracensis DSM 15199GCA_001010285completencbi230089
66792Photorhabdus temperata subsp. thracensis strain DSM 15199230089.6completepatric230089
66792Photorhabdus thracensis:DSM 151992639762814completeimg230089

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.26no
flagellatedyes70.109no
gram-positiveno98.33no
anaerobicno98.115no
aerobicyes81.898no
halophileno86.511no
spore-formingno94.241no
thermophileno98yes
glucose-utilyes90.667no
glucose-fermentyes83.649no

External links

@ref: 5752

culture collection no.: DSM 15199, CIP 108426, NCIMB 13952

straininfo link

  • @ref: 74539
  • straininfo: 97531

Reference

@idauthorscataloguedoi/urltitle
5752Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15199)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15199
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
33988Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6047
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)
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
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
74539Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97531.1StrainInfo: A central database for resolving microbial strain identifiers
123534Curators of the CIPCollection of Institut Pasteur (CIP 108426)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108426