Strain identifier

BacDive ID: 11735

Type strain: Yes

Species: Pasteurella dagmatis

Strain Designation: SDH 953/60, 953/60

Strain history: CIP <- 1989, NCTC <- R. Mutters, Phillipps Univ., Marburg, Germany <- W. Frederiksen, Stat. Ser., Copenhagen, Denmark <- S.D. Henriksen, Oslo, Norway : strain 953/60

NCBI tax ID(s): 667128 (strain), 754 (species)

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General

@ref: 16565

BacDive-ID: 11735

DSM-Number: 22969

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

description: Pasteurella dagmatis SDH 953/60 is a mesophilic, Gram-negative bacterium that was isolated from human respiratory tract.

NCBI tax id

NCBI tax idMatching level
754species
667128strain

strain history

@refhistory
16565<- CCUG <- W. Frederiksen, Statens Serum Inst., Copenhagen, Denmark <- S. D. Hendriksen; SDH 953/60
118850CIP <- 1989, NCTC <- R. Mutters, Phillipps Univ., Marburg, Germany <- W. Frederiksen, Stat. Ser., Copenhagen, Denmark <- S.D. Henriksen, Oslo, Norway : strain 953/60

doi: 10.13145/bacdive11735.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Pasteurella
  • species: Pasteurella dagmatis
  • full scientific name: Pasteurella dagmatis Mutters et al. 1985

@ref: 16565

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Pasteurella

species: Pasteurella dagmatis

full scientific name: Pasteurella dagmatis Mutters et al. 1985

strain designation: SDH 953/60, 953/60

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.917

colony morphology

  • @ref: 16565
  • type of hemolysis: alpha
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16565COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
40589MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicolayesDistilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)
118850CIP Medium 118-byeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b

culture temp

@refgrowthtypetemperaturerange
16565positivegrowth37mesophilic
40589positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
68368L-arabinose-fermentation30849
68368amygdalin-fermentation27613
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea+hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
68374ornithine-degradation18257
68374arginine-hydrolysis29016
68374lysine-degradation25094
68374urea-hydrolysis16199
68374L-arabitol-builds acid from18403
68374D-galacturonic acid-builds acid from18024
68374Potassium 5-ketogluconate-builds acid from
68374D-mannitol-builds acid from16899
68374maltose-builds acid from17306
68374ribitol-builds acid from15963
68374palatinose-builds acid from18394
68374malonate-assimilation15792
68374tryptophan+energy source27897
68374D-glucose-builds acid from17634
68374sucrose-builds acid from17992
68374L-arabinose-builds acid from30849
68374D-arabitol-builds acid from18333
68374trehalose-builds acid from27082
68374L-rhamnose-builds acid from62345
68374myo-inositol-builds acid from17268
68374cellobiose-builds acid from17057
68374sorbitol-builds acid from30911
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68381arginine-hydrolysis29016
68381D-ribose+builds acid from16988
68381D-mannitol-builds acid from16899
68381sorbitol-builds acid from30911
68381lactose-builds acid from17716
68381trehalose+builds acid from27082
68381raffinose-builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside-builds acid from320055
68381D-tagatose-builds acid from16443
68381urea+hydrolysis16199

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6837435581indole+
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
16565catalase+1.11.1.6
16565cytochrome-c oxidase+1.9.3.1
68381urease+3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase-3.2.1.23
68374L-aspartate arylamidase+3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
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
45689-+---+----+----+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
45689------+-++-+--------+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
45689--------------------------------------------------
45689-------------------------------------------------+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
45689--------+-------+--------------+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
16565++++-+-+---+-
16565-++++-+-+---+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
16565-----++---+-+------------+-----+
45689-----++---+-+------------+-----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16565human respiratory tractNorwayNOREurope
45689Human respiratory tract
118850Human, Nose

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_7934.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_298;97_4511;98_5791;99_7934&stattab=map
  • Last taxonomy: Pasteurella dagmatis subclade
  • 16S sequence: AY362920
  • Sequence Identity:
  • Total samples: 1975
  • soil counts: 4
  • aquatic counts: 26
  • animal counts: 1939
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
165652Risk group (German classification)
1188502Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pasteurella dagmatis ATCC 43325 16S ribosomal RNA gene, partial sequenceM750511486ena667128
16565Pasteurella dagmatis ATCC 43325 strain CCUG 12397 16S ribosomal RNA gene, partial sequenceAY3629201364ena667128

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pasteurella dagmatis NCTC11617GCA_900186835completencbi754
66792Pasteurella dagmatis ATCC 43325GCA_000163475scaffoldncbi667128
66792Pasteurella dagmatis ATCC 43325667128.3wgspatric667128
66792Pasteurella dagmatis strain NCTC11617754.3completepatric754
66792Pasteurella dagmatis NCTC 116172773857813completeimg754
66792Pasteurella dagmatis ATCC 43325647000288draftimg667128

GC content

  • @ref: 16565
  • GC-content: 40.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.8no
flagellatedno94.47no
gram-positiveno98.769no
anaerobicno96.56no
aerobicno92.192no
halophileno60.772no
spore-formingno98.665no
thermophileno97.289yes
glucose-utilno62.016no
glucose-fermentyes56.196yes

External links

@ref: 16565

culture collection no.: DSM 22969, ATCC 43325, CCUG 12397, CIP 103293, NCTC 11617

straininfo link

  • @ref: 80954
  • straininfo: 41774

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16565Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22969)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22969
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
40589Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15074
45689Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12397)https://www.ccug.se/strain?id=12397
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68374Automatically annotated from API ID32E
68377Automatically annotated from API NH
68381Automatically annotated from API rID32STR
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
80954Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41774.1StrainInfo: A central database for resolving microbial strain identifiers
118850Curators of the CIPCollection of Institut Pasteur (CIP 103293)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103293