Strain identifier

BacDive ID: 11693

Type strain: Yes

Species: Avibacterium endocarditidis

Strain Designation: 20186H4H1

Strain history: CIP <- 2007, CCUG <- 2006, H. Crhistensen, Copenhagen Univ., Frederiksberg, Denmark: strain 20186H4H1

NCBI tax ID(s): 380674 (species)

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General

@ref: 7440

BacDive-ID: 11693

DSM-Number: 18224

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

description: Avibacterium endocarditidis 20186H4H1 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from chicken, valvular endocarditis.

NCBI tax id

  • NCBI tax id: 380674
  • Matching level: species

strain history

@refhistory
7440<- H. Christensen; 20186H4H1 <- M. Bisgaard
119025CIP <- 2007, CCUG <- 2006, H. Crhistensen, Copenhagen Univ., Frederiksberg, Denmark: strain 20186H4H1

doi: 10.13145/bacdive11693.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Avibacterium
  • species: Avibacterium endocarditidis
  • full scientific name: Avibacterium endocarditidis Bisgaard et al. 2007

@ref: 7440

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Avibacterium

species: Avibacterium endocarditidis

full scientific name: Avibacterium endocarditidis Bisgaard et al. 2007

strain designation: 20186H4H1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32050negativerod-shapedno
69480negative99.73
119025negativerod-shapedno

colony morphology

  • @ref: 59690
  • incubation period: 1 day

pigmentation

  • @ref: 32050
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7440COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
37433MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119025CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119025CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
7440positivegrowth37mesophilic
32050positiveoptimum37mesophilic
37433positivegrowth37mesophilic
59690positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32050aerobe
59690aerobe
119025facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3205023652dextrin+carbon source
3205028757fructose+carbon source
3205028260galactose+carbon source
3205024265gluconate+carbon source
3205017234glucose+carbon source
3205017754glycerol+carbon source
3205025115malate+carbon source
3205017306maltose+carbon source
3205029864mannitol+carbon source
32050506227N-acetylglucosamine+carbon source
3205016634raffinose+carbon source
3205033942ribose+carbon source
3205030911sorbitol+carbon source
3205017992sucrose+carbon source
3205027082trehalose+carbon source
3205017632nitrate+reduction
11902517632nitrate+reduction
11902516301nitrite+reduction
6837717634D-glucose+builds acid from
6837715824D-fructose+builds acid from
6837717306maltose+builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
11902535581indoleno

metabolite tests

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32050acid phosphatase+3.1.3.2
32050alkaline phosphatase+3.1.3.1
32050alpha-galactosidase+3.2.1.22
32050catalase+1.11.1.6
32050cytochrome oxidase+1.9.3.1
32050urease+3.5.1.5
68377tryptophan deaminase-4.1.99.1
68377alkaline phosphatase+3.1.3.1
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
119025oxidase+
119025catalase+1.11.1.6
119025urease-3.5.1.5

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
7440++++---++-+--
7440-++++---++-+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
7440chicken, valvular endocarditisDenmarkDNKEurope
59690Adult broiler parent hen,valvular endocarditisDenmarkDNKEurope2004Copenhagen,RVAU
119025Valvular endocarditis, adult broiler parentDenmarkDNKEuropeCopenhagen2004

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Birds#Chicken

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7440yes2Risk group (German classification)
1190251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7440
  • description: Avibacterium endocarditidis strain 20186H4H1 16S ribosomal RNA gene, partial sequence
  • accession: DQ465412
  • length: 1218
  • database: ena
  • NCBI tax ID: 380674

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Avibacterium endocarditidis 20186H4H1GCA_002921145scaffoldncbi380674
66792Avibacterium endocarditidis 20186H4H12842990487draftimg380674

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.202no
gram-positiveno98.489yes
anaerobicno97.799no
aerobicno92.331yes
halophileyes51.408no
spore-formingno98.798no
glucose-utilno50no
thermophileno98.999yes
motileno89.952yes
glucose-fermentno51.472no

External links

@ref: 7440

culture collection no.: CIP 109717, DSM 18224, CCUG 52860

straininfo link

  • @ref: 80913
  • straininfo: 309431

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684246
  • title: Avibacterium endocarditidis sp. nov., isolated from valvular endocarditis in chickens.
  • authors: Bisgaard M, Christensen JP, Bojesen AM, Christensen H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64879-0
  • year: 2007
  • mesh: Animals, Chickens, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Endocarditis, Bacterial/microbiology/*veterinary, Heart Valves/microbiology, Molecular Sequence Data, Pasteurellaceae/genetics/*isolation & purification/metabolism, Phylogeny, Poultry Diseases/*microbiology, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7440Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18224)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18224
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
32050Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2830028776041
37433Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7491
59690Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52860)https://www.ccug.se/strain?id=52860
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)
68377Automatically annotated from API NH
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
80913Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309431.1StrainInfo: A central database for resolving microbial strain identifiers
119025Curators of the CIPCollection of Institut Pasteur (CIP 109717)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109717