Strain identifier

BacDive ID: 5034

Type strain: Yes

Species: Photorhabdus temperata

Strain Designation: XlNach, X1Nach

Strain history: CIP <- 1998, N. Boemare, Univ. Montpellier II, Lab. Pathol. comparée, Montpellier, France: strain X1Nach <- R.J. Akhurst <- Spiridonov

NCBI tax ID(s): 574560 (species)

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General

@ref: 5383

BacDive-ID: 5034

DSM-Number: 14550

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped, animal pathogen

description: Photorhabdus temperata XlNach is an obligate aerobe, mesophilic, Gram-negative animal pathogen that was isolated from nematode Heterorhabditis megidis.

NCBI tax id

  • NCBI tax id: 574560
  • Matching level: species

strain history

@refhistory
5383<- CIP <- N. Boemare, Univ. Montpellier; XlNach <- R. J. Akhurst <- Spiridonov
123442CIP <- 1998, N. Boemare, Univ. Montpellier II, Lab. Pathol. comparée, Montpellier, France: strain X1Nach <- R.J. Akhurst <- Spiridonov

doi: 10.13145/bacdive5034.20230509.8.1

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 temperata
  • full scientific name: Photorhabdus temperata Fischer-Le Saux et al. 1999

@ref: 5383

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus temperata

full scientific name: Photorhabdus temperata Fischer-Le Saux et al. 1999 emend. Machado et al. 2018

strain designation: XlNach, X1Nach

type strain: yes

Morphology

cell morphology

  • @ref: 123442
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5383COLUMBIA AGAR (DSMZ Medium 715)yeshttps://mediadive.dsmz.de/medium/715Name: COLUMBIA AGAR (DSMZ Medium 715) Composition: Peptone mixture 23.0 g/l Agar 10.0 g/l NaCl 5.0 g/l Starch 1.0 g/l Distilled water
5383TRYPTICASE 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
38563MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123442CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5383positivegrowth30mesophilic
38563positivegrowth30mesophilic
123442positivegrowth30mesophilic
123442nogrowth5psychrophilic
123442nogrowth10psychrophilic
123442nogrowth37mesophilic
123442nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123442
  • oxygen tolerance: obligate aerobe

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
123442mannitol-fermentation29864
123442citrate-carbon source16947
123442esculin+hydrolysis4853
123442glucose+fermentation17234
123442lactose-fermentation17716
123442nitrate-reduction17632
123442nitrite-reduction16301
123442malonate-assimilation15792
123442sodium thiosulfate-builds gas from132112
123442glucose+degradation17234

antibiotic resistance

  • @ref: 123442
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123442
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12344215688acetoin-
12344217234glucose-

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
123442oxidase-
123442beta-galactosidase-3.2.1.23
123442alcohol dehydrogenase-1.1.1.1
123442gelatinase+/-
123442amylase-
123442DNase-
123442caseinase+3.4.21.50
123442catalase+1.11.1.6
123442tween esterase-
123442lecithinase-
123442lipase-
123442lysine decarboxylase-4.1.1.18
123442ornithine decarboxylase-4.1.1.17
123442phenylalanine ammonia-lyase-4.3.1.24
123442protease+
123442tryptophan deaminase-
123442urease-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
123442--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123442----------++---------+---------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123442---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5383nematode Heterorhabditis megidisHeterorhabditis megidisNachodkaRussiaRUS
123442Animal, Nematode Heterorhabditis megidisNakhodkaRussian FederationRUSEurope1984

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1261;98_3054;99_4030&stattab=map
  • Last taxonomy: Photorhabdus temperata subclade
  • 16S sequence: AJ007405
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 5
  • aquatic counts: 2
  • animal counts: 26

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5383yes1Risk group (German classification)
1234421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5383
  • description: Photorhabdus temperata partial 16S rRNA gene, strain XINach
  • accession: AJ007405
  • length: 1526
  • database: ena
  • NCBI tax ID: 574560

Genome sequences

  • @ref: 66792
  • description: Photorhabdus temperata DSM 14550
  • accession: GCA_025384845
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 574560

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.482no
flagellatedyes63.902no
gram-positiveno98.188no
anaerobicno98.183no
aerobicyes86.418no
halophileno86.424no
spore-formingno93.799no
glucose-fermentyes82.266no
thermophileno99.046yes
glucose-utilyes91.988no

External links

@ref: 5383

culture collection no.: DSM 14550, CCM 7078, CIP 105563

straininfo link

  • @ref: 74529
  • straininfo: 69653

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Genetics24642011Structure of the O-polysaccharide of Photorhabdus temperata subsp. temperata XlNach(T) containing a novel branched monosaccharide, 3,6-dideoxy-4-C-[(S)-1,2-dihydroxyethyl]-d-xylo-hexose.Arbatsky NP, Shashkov AS, Kirsheva NA, Kondakova AN, Shaikhutdinova RZ, Ivanov SA, Anisimov AP, Knirel YACarbohydr Res10.1016/j.carres.2014.02.0202014Carbohydrate Sequence, Hexoses/*chemistry, Molecular Sequence Data, Photorhabdus/*chemistry, Polysaccharides, Bacterial/*chemistry

Reference

@idauthorscataloguedoi/urltitle
5383Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14550)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14550
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
38563Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17596
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
74529Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID69653.1StrainInfo: A central database for resolving microbial strain identifiers
123442Curators of the CIPCollection of Institut Pasteur (CIP 105563)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105563