Strain identifier

BacDive ID: 5050

Type strain: Yes

Species: Photorhabdus hainanensis

Strain Designation: C8404

Strain history: CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain C8404

NCBI tax ID(s): 1004166 (species)

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General

@ref: 16317

BacDive-ID: 5050

DSM-Number: 22397

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

description: Photorhabdus hainanensis C8404 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from Heterorhabditis species.

NCBI tax id

  • NCBI tax id: 1004166
  • Matching level: species

strain history

@refhistory
16317<- P. Tailliez, INRA, Univ. Montpellier, France; C8404 <- N. E. Boemare <- R. J. Akhurst
119787CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain C8404

doi: 10.13145/bacdive5050.20230509.8.1

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 hainanensis
  • full scientific name: Photorhabdus hainanensis (Tailliez et al. 2010) Machado et al. 2018

  • synonyms

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

@ref: 16317

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Photorhabdus

species: Photorhabdus hainanensis

full scientific name: Photorhabdus hainanensis (Tailliez et al. 2010) Machado et al. 2018

strain designation: C8404

type strain: yes

Morphology

cell morphology

  • @ref: 119787
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16317REACTIVATION 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
37889MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119787CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16317positivegrowth28mesophilic
37889positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119787
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11978717632nitrate-reduction
11978716301nitrite-reduction

metabolite production

  • @ref: 119787
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
119787oxidase-
119787catalase+1.11.1.6
119787urease-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
119787-+---++-+-++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
16317Heterorhabditis speciesHeterorhabditisHainan islandChinaCHNAsia
119787Animal, Nematode, Heterorhabditis sp.Hainan IslandChinaCHNAsia1992

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2957.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1046;97_1857;98_2282;99_2957&stattab=map
  • Last taxonomy: Photorhabdus
  • 16S sequence: EU930342
  • Sequence Identity:
  • Total samples: 11
  • soil counts: 1
  • aquatic counts: 1
  • animal counts: 3
  • plant counts: 6

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16317yes1Risk group (German classification)
1197871Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16317
  • description: Photorhabdus luminescens strain C8404 16S ribosomal RNA gene, partial sequence
  • accession: EU930342
  • length: 1379
  • database: ena
  • NCBI tax ID: 1004166

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photorhabdus hainanensis DSM 22397GCA_018448965scaffoldncbi1004166
66792Photorhabdus hainanensis strain DSM 223971004166.3wgspatric1004166

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.512no
flagellatedyes55.54no
gram-positiveno98.339no
anaerobicno97.973no
aerobicyes84.658no
halophileno87.43no
spore-formingno93.866no
thermophileno98.055yes
glucose-utilyes92.776no
glucose-fermentyes84.647no

External links

@ref: 16317

culture collection no.: DSM 22397, CIP 109946, CN 8404

straininfo link

  • @ref: 74545
  • straininfo: 370406

Reference

@idauthorscataloguedoi/urltitle
16317Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22397)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22397
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
37889Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7747
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)
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
74545Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370406.1StrainInfo: A central database for resolving microbial strain identifiers
119787Curators of the CIPCollection of Institut Pasteur (CIP 109946)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109946