Strain identifier

BacDive ID: 11694

Type strain: Yes

Species: Avibacterium paragallinarum

Strain history: CIP <- 1990, NCTC <- 1979, K.H. Hinz, Hannover, Germany: strain IPDH 2403

NCBI tax ID(s): 728 (species)

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General

@ref: 7586

BacDive-ID: 11694

DSM-Number: 18554

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

description: Avibacterium paragallinarum DSM 18554 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from infraorbital sinus of a chicken.

NCBI tax id

  • NCBI tax id: 728
  • Matching level: species

strain history

@refhistory
7586<- CCM <- K.-H. Hinz; IPDH 2403
121558CIP <- 1990, NCTC <- 1979, K.H. Hinz, Hannover, Germany: strain IPDH 2403

doi: 10.13145/bacdive11694.20230509.8.1

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 paragallinarum
  • full scientific name: Avibacterium paragallinarum (Biberstein and White 1969) Blackall et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Haemophilus paragallinarum

@ref: 7586

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Avibacterium

species: Avibacterium paragallinarum

full scientific name: Avibacterium paragallinarum (Biberstein and White 1969) Blackall et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 121558
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@reftype of hemolysisincubation period
7586gamma3-7 days
458372 days
121558

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7586CHOCOLATE AGAR (DSMZ Medium 429b)yeshttps://mediadive.dsmz.de/medium/429bName: CHOCOLATE AGAR (DSMZ Medium 429b) Composition: Horse blood 100.0 g/l Sheep blood 100.0 g/l Columbia agar base
34281MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
121558CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
7586positivegrowth37mesophilic
34281positivegrowth37mesophilic
45837positivegrowth37mesophilic
121558positivegrowth30-41
121558nogrowth15psychrophilic
121558nogrowth25mesophilic
121558nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7586microaerophile
45837microaerophile
121558facultative 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
121558esculin-hydrolysis4853
121558hippurate-hydrolysis606565
121558nitrate-reduction17632
121558nitrite-reduction16301
68377D-glucose+builds acid from17634
68377ornithine-degradation18257
68377urea-hydrolysis16199
68377tryptophan-energy source27897

antibiotic resistance

  • @ref: 121558
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12155835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
7586catalase-1.11.1.6
7586cytochrome-c oxidase+1.9.3.1
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase-3.2.1.23
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
121558oxidase+
121558beta-galactosidase+3.2.1.23
121558alcohol dehydrogenase-1.1.1.1
121558catalase-1.11.1.6
121558gamma-glutamyltransferase+2.3.2.2
121558lysine decarboxylase-4.1.1.18
121558ornithine decarboxylase-4.1.1.17
121558urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121558-+---+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121558-------------------------------------------------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
7586++-+---+-----
7586++-+/----+-----
7586-++++---+----
7586-++-+---+----
7586-++-+/----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7586infraorbital sinus of a chickenGermanyDEUEurope
45837Chick,infraorbital sinusGermanyDEUEurope
121558Animal, Chick, infraorbital sinusGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_3997.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_2031;97_2447;98_3028;99_3997&stattab=map
  • Last taxonomy: Avibacterium paragallinarum
  • 16S sequence: AY498868
  • Sequence Identity:
  • Total samples: 5157
  • soil counts: 14
  • aquatic counts: 126
  • animal counts: 5012
  • plant counts: 5

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7586yes2Risk group (German classification)
1215582Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7586
  • description: Haemophilus paragallinarum strain NCTC 11296T 16S ribosomal RNA gene, partial sequence
  • accession: AY498868
  • length: 1463
  • database: ena
  • NCBI tax ID: 728

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Avibacterium paragallinarum NCTC11296GCA_900450705contigncbi728
66792Avibacterium paragallinarum CCUG 12835GCA_002921155contigncbi728
66792Avibacterium paragallinarum strain CCUG 12835728.90wgspatric728
66792Avibacterium paragallinarum strain NCTC11296728.107wgspatric728
66792Avibacterium paragallinarum NCTC 112962823233258draftimg728
66792Avibacterium paragallinarum CCUG 128352837414230draftimg728

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.383no
flagellatedno95.137no
gram-positiveno98.805no
anaerobicno97.867no
aerobicno93.637yes
halophileno51.123no
spore-formingno98.88no
thermophileno97.706yes
glucose-utilyes53.946no
glucose-fermentyes57.019no

External links

@ref: 7586

culture collection no.: DSM 18554, CCM 6075, CCUG 12835, CIP 103453, HIM 668-7, ATCC 29545, NCTC 11296, IPDH 2403

straininfo link

  • @ref: 80914
  • straininfo: 45865

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653900Reclassification of Pasteurella gallinarum, [Haemophilus] paragallinarum, Pasteurella avium and Pasteurella volantium as Avibacterium gallinarum gen. nov., comb. nov., Avibacterium paragallinarum comb. nov., Avibacterium avium comb. nov. and Avibacterium volantium comb. nov.Blackall PJ, Christensen H, Beckenham T, Blackall LL, Bisgaard MInt J Syst Evol Microbiol10.1099/ijs.0.63357-02005Animals, Bacterial Typing Techniques, Bird Diseases/microbiology, Chickens/microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Haemophilus Infections/microbiology/veterinary, Haemophilus paragallinarum/*classification/genetics, Molecular Sequence Data, Pasteurella/*classification/genetics, Pasteurellaceae/*classification/genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Enzymology19729253Evaluation of two experimental infection models for Avibacterium paragallinarum.Zhao Q, Sun YN, Zhang XX, Kong YB, Xie ZJ, Zhu YL, Zhou EM, Jiang SJVet Microbiol10.1016/j.vetmic.2009.07.0342009Animals, Chickens/microbiology, Disease Models, Animal, Pasteurellaceae/genetics/isolation & purification/*pathogenicity, Pasteurellaceae Infections/*microbiology/pathology, Polymerase Chain Reaction, Poultry Diseases/*microbiology/pathology, Random AllocationPhylogeny
Enzymology31347465Validation of a real-time PCR assay for high-throughput detection of Avibacterium paragallinarum in chicken respiratory sites.Clothier KA, Stoute S, Torain A, Crossley BJ Vet Diagn Invest10.1177/10406387198664842019Animals, Chickens/*microbiology, Common Cold/microbiology/veterinary, Haemophilus Infections/microbiology/*veterinary, Haemophilus paragallinarum/genetics/*isolation & purification, High-Throughput Nucleotide Sequencing/veterinary, Nasopharynx/microbiology, Paranasal Sinuses/microbiology, Pasteurellaceae, Poultry Diseases/diagnosis/*microbiology, Real-Time Polymerase Chain Reaction/*veterinary, Trachea/microbiologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7586Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18554)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18554
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
34281Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15252
45837Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12835)https://www.ccug.se/strain?id=12835
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68377Automatically annotated from API NH
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
80914Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45865.1StrainInfo: A central database for resolving microbial strain identifiers
121558Curators of the CIPCollection of Institut Pasteur (CIP 103453)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103453