Strain identifier

BacDive ID: 4357

Type strain: Yes

Species: Edwardsiella hoshinae

Strain Designation: 2-78

Strain history: CIP <- 1978, C. Richard, Inst. Pasteur, Paris, France: strain 2-78

NCBI tax ID(s): 1216966 (strain), 93378 (species)

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General

@ref: 5158

BacDive-ID: 4357

DSM-Number: 13771

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

description: Edwardsiella hoshinae 2-78 is a facultative anaerobe, mesophilic, Gram-negative human pathogen that was isolated from dead female puffin.

NCBI tax id

NCBI tax idMatching level
1216966strain
93378species

strain history

@refhistory
5158<- CIP <- C. Richard, Inst. Pasteur; 2-78
67770Y. Kosako 82074 <-- R. Sakazaki 136 <-- P. A. D. Grimont 2-78.
119975CIP <- 1978, C. Richard, Inst. Pasteur, Paris, France: strain 2-78

doi: 10.13145/bacdive4357.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Hafniaceae
  • genus: Edwardsiella
  • species: Edwardsiella hoshinae
  • full scientific name: Edwardsiella hoshinae Grimont et al. 1981

@ref: 5158

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Hafniaceae

genus: Edwardsiella

species: Edwardsiella hoshinae

full scientific name: Edwardsiella hoshinae Grimont et al. 1981

strain designation: 2-78

type strain: yes

Morphology

cell morphology

  • @ref: 119975
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5158CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
5158BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
34388MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119975CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5158positivegrowth30mesophilic
34388positivegrowth30mesophilic
67770positivegrowth37mesophilic
119975positivegrowth30-41
119975nogrowth5psychrophilic
119975nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119975
  • 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
119975mannitol+fermentation29864
119975citrate-carbon source16947
119975glucose+fermentation17234
119975lactose-fermentation17716
119975nitrate+reduction17632
119975nitrite-reduction16301
119975malonate-assimilation15792
119975sodium thiosulfate+builds gas from132112

metabolite production

  • @ref: 119975
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11997515688acetoin-
11997517234glucose+

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
119975oxidase-
119975beta-galactosidase-3.2.1.23
119975alcohol dehydrogenase-1.1.1.1
119975gelatinase-
119975catalase+1.11.1.6
119975lysine decarboxylase+4.1.1.18
119975ornithine decarboxylase+4.1.1.17
119975phenylalanine ammonia-lyase-4.3.1.24
119975tryptophan deaminase-
119975urease-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
119975-++--+----++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119975+---+----++++----+---+-----+--++-----------+--+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119975+++++--+-++------+-+----+------+------------------------------+--+---------+----------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5158dead female puffinCôtes d'ArmorFranceFRAEurope
67770Female puffin
119975Animal, Dead female shearwater (bird)Côtes d'ArmorFranceFRAEurope1978

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host#Other#Decomposing animal

taxonmaps

  • @ref: 69479
  • File name: preview.99_47.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_38;97_40;98_44;99_47&stattab=map
  • Last taxonomy: Edwardsiella
  • 16S sequence: AB050825
  • Sequence Identity:
  • Total samples: 22716
  • soil counts: 509
  • aquatic counts: 2305
  • animal counts: 19360
  • plant counts: 542

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5158yes, in single cases1Risk group (German classification)
1199751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Edwardsiella hoshinae gene for 16S rRNA, partial sequence
  • accession: AB050825
  • length: 1466
  • database: ena
  • NCBI tax ID: 93378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Edwardsiella hoshinae NCTC12121GCA_900447315contigncbi93378
66792Edwardsiella hoshinae NBRC 1056991216966.6wgspatric1216966
66792Edwardsiella hoshinae strain FDAARGOS_94093378.7completepatric93378
66792Edwardsiella hoshinae strain NCTC1212193378.6wgspatric93378
66792Edwardsiella hoshinae NCTC 121212851255004draftimg93378
66792Edwardsiella hoshinae NBRC 1056992563367140draftimg1216966
67770Edwardsiella hoshinae NBRC 105699 = ATCC 33379GCA_000474215contigncbi1216966

GC content

  • @ref: 67770
  • GC-content: 55.6-55.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.136no
flagellatedyes57.468no
gram-positiveno98.711no
anaerobicno82.123no
halophileno85.466no
spore-formingno96.627no
glucose-utilyes90.301no
aerobicno51.066no
thermophileno97.761yes
glucose-fermentyes91.64no

External links

@ref: 5158

culture collection no.: DSM 13771, ATCC 33379, CIP 78.56, JCM 1679, NCTC 12121, CCUG 14800, NBRC 105699

straininfo link

  • @ref: 73848
  • straininfo: 389449

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5158Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13771
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
34388Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11006
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
73848Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389449.1StrainInfo: A central database for resolving microbial strain identifiers
119975Curators of the CIPCollection of Institut Pasteur (CIP 78.56)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2078.56