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/bacdive11693.20250331.9.3

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
119025negativerod-shapedno
125439negative98.3
125438no92.376
125438negative98.5

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

@refgrowthtypetemperature
7440positivegrowth37
32050positiveoptimum37
37433positivegrowth37
59690positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32050aerobe
59690aerobe
119025facultative anaerobe
125439obligate aerobe99.1

spore formation

@refspore formationconfidence
125439no97.5
125438no93.547

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
6837727897tryptophan-energy source
6837716199urea-hydrolysis
6837718257ornithine-degradation
6837717306maltose+builds acid from
6837715824D-fructose+builds acid from
6837717634D-glucose+builds acid from
11902517632nitrate+reduction
11902516301nitrite+reduction

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
119025oxidase+
119025catalase+1.11.1.6
119025urease-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

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: nuccore
  • NCBI tax ID: 380674

Genome sequences

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

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.448no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no84.528no
125438spore-formingspore-formingAbility to form endo- or exosporesno93.547no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementno92.376no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.5
125439BacteriaNetmotilityAbility to perform movementno72.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.1

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1