Strain identifier

BacDive ID: 5625

Type strain: Yes

Species: Ornithobacterium rhinotracheale

Strain Designation: 11-14-5

Strain history: CIP <- 1994, LMG <- CCUG <- M. Bisgaard: strain 11-14-5 <- C. Baxter-Jones

NCBI tax ID(s): 867902 (strain), 28251 (species)

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General

@ref: 6230

BacDive-ID: 5625

DSM-Number: 15997

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

description: Ornithobacterium rhinotracheale 11-14-5 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from turkey, respiratory tract.

NCBI tax id

NCBI tax idMatching level
28251species
867902strain

strain history

@refhistory
6230<- CCUG <- M. Bisgaard <- Baxter-Jones
122197CIP <- 1994, LMG <- CCUG <- M. Bisgaard: strain 11-14-5 <- C. Baxter-Jones

doi: 10.13145/bacdive5625.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Ornithobacterium
  • species: Ornithobacterium rhinotracheale
  • full scientific name: Ornithobacterium rhinotracheale Vandamme et al. 1994

@ref: 6230

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Ornithobacterium

species: Ornithobacterium rhinotracheale

full scientific name: Ornithobacterium rhinotracheale Vandamme et al. 1994

strain designation: 11-14-5

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.964
122197negativerod-shapedno

colony morphology

  • @ref: 122197

multimedia

@refmultimedia contentintellectual property rightscaption
6230https://www.dsmz.de/microorganisms/photos/DSM_15997.jpg© Leibniz-Institut DSMZ
66793EM_DSM_15997_1.jpg© HZI/Manfred Rohdeelectron microscopic image

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6230TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
40924MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122197CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6230positivegrowth35mesophilic
40924positivegrowth37mesophilic
122197positivegrowth30-41
122197nogrowth5psychrophilic
122197nogrowth15psychrophilic
122197nogrowth25mesophilic
122197nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6230microaerophile
122197obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
122197NaClnogrowth0 %
122197NaClnogrowth2 %
122197NaClnogrowth4 %
122197NaClnogrowth6 %
122197NaClnogrowth8 %
122197NaClnogrowth10 %

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
122197citrate-carbon source16947
122197esculin-hydrolysis4853
122197hippurate+hydrolysis606565
122197nitrate-builds gas from17632
122197nitrate-reduction17632
122197nitrite-builds gas from16301
122197nitrite-reduction16301
122197malonate-assimilation15792
122197glucose+/-degradation17234
122197nitrate-respiration17632
68377D-glucose-builds acid from17634
68377D-fructose-builds acid from15824
68377maltose-builds acid from17306
68377sucrose-builds acid from17992
68377ornithine-degradation18257
68377urea-hydrolysis16199
68377tryptophan-energy source27897

antibiotic resistance

  • @ref: 122197
  • 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
12219735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
12219715688acetoin+
12219717234glucose-

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
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase+3.1.3.1
68377lipase+
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
122197oxidase+
122197beta-galactosidase+3.2.1.23
122197alcohol dehydrogenase-1.1.1.1
122197gelatinase-
122197amylase-
122197DNase-
122197caseinase-3.4.21.50
122197catalase-1.11.1.6
122197tween esterase-
122197gamma-glutamyltransferase-2.3.2.2
122197lecithinase-
122197lipase-
122197lysine decarboxylase-4.1.1.18
122197ornithine decarboxylase-4.1.1.17
122197phenylalanine ammonia-lyase-4.3.1.24
122197tryptophan deaminase-
122197urease-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
122197-+++++++--++++-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122197-------------------------------------------------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
6230-------++++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122197---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
6230turkey, respiratory tractUnited KingdomGBREurope
47759Turkey,respiratory tract infectionUnited KingdomGBREurope1988
122197Turkey, respiratory tractUnited KingdomGBREurope1988

isolation source categories

Cat1Cat2
#Host#Birds
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_4530.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_472;96_2264;97_2743;98_3406;99_4530&stattab=map
  • Last taxonomy: Ornithobacterium rhinotracheale subclade
  • 16S sequence: U87101
  • Sequence Identity:
  • Total samples: 1929
  • soil counts: 169
  • aquatic counts: 906
  • animal counts: 811
  • plant counts: 43

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6230yes2Risk group (German classification)
1221971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ornithobacterium rhinotracheale 16S ribosomal RNA gene, complete sequenceU871011462ena867902
6230Ornithobacterium rhinotracheale 16S ribosomal RNAL191561451ena28251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithobacterium rhinotracheale DSM 15997GCA_000265465completencbi867902
66792Ornithobacterium rhinotracheale DSM 15997867902.3completepatric867902
66792Ornithobacterium rhinotracheale DSM 159972509601001completeimg867902

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.006no
flagellatedno94.083no
gram-positiveno97.227no
anaerobicno96.485yes
aerobicno92.107yes
halophileno76.279no
spore-formingno96.73no
thermophileno98.288yes
glucose-utilyes87.291no
glucose-fermentno71.087no

External links

@ref: 6230

culture collection no.: DSM 15997, CCUG 23171, LMG 9086, MCCM 01774, CIP 104009, ATCC 51463

straininfo link

  • @ref: 75108
  • straininfo: 7798

literature

  • topic: Metabolism
  • Pubmed-ID: 23062950
  • title: Ornithobacterium rhinotracheale has neuraminidase activity causing desialylation of chicken and turkey serum and tracheal mucus glycoproteins.
  • authors: Kastelic S, Bercic RL, Cizelj I, Bencina M, Makrai L, Zorman-Rojs O, Narat M, Bisgaard M, Christensen H, Bencina D
  • journal: Vet Microbiol
  • DOI: 10.1016/j.vetmic.2012.09.018
  • year: 2012
  • mesh: Animals, Blood Proteins/metabolism, Chickens, Flavobacteriaceae Infections/blood/enzymology/metabolism/*veterinary, Glycoproteins/metabolism, Hungary, Immunoglobulin G/metabolism, Mucus/metabolism, N-Acetylneuraminic Acid/analogs & derivatives/metabolism/pharmacology, Neuraminidase/antagonists & inhibitors/genetics/*metabolism, Ornithobacterium/*enzymology/genetics, Poultry Diseases/blood/enzymology/*metabolism/*microbiology, Trachea/metabolism, Transferrin/metabolism, Turkeys
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6230Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15997)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15997
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
40924Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15870
47759Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23171)https://www.ccug.se/strain?id=23171
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
75108Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7798.1StrainInfo: A central database for resolving microbial strain identifiers
122197Curators of the CIPCollection of Institut Pasteur (CIP 104009)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104009