Strain identifier

BacDive ID: 5634

Type strain: Yes

Species: Riemerella columbipharyngis

Strain Designation: 8151, RCP-8151

Strain history: <- D. Rubbenstroth, University of Veterinary Medicine Hannover, Clinic for Poultry, Germany; RCP-8151

NCBI tax ID(s): 1071918 (species)

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General

@ref: 17476

BacDive-ID: 5634

DSM-Number: 24015

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

description: Riemerella columbipharyngis 8151 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from pharynx of a apparently healthy feral pigeon Columba livia f. domestica.

NCBI tax id

  • NCBI tax id: 1071918
  • Matching level: species

strain history

  • @ref: 17476
  • history: <- D. Rubbenstroth, University of Veterinary Medicine Hannover, Clinic for Poultry, Germany; RCP-8151

doi: 10.13145/bacdive5634.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Riemerella
  • species: Riemerella columbipharyngis
  • full scientific name: Riemerella columbipharyngis Rubbenstroth et al. 2013

@ref: 17476

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Riemerella

species: Riemerella columbipharyngis

full scientific name: Riemerella columbipharyngis Rubbenstroth et al. 2013

strain designation: 8151, RCP-8151

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30469negative1.75 µm0.35 µmrod-shapedno
69480negative99.806

colony morphology

  • @ref: 17476
  • type of hemolysis: gamma
  • incubation period: 1-2 days

pigmentation

  • @ref: 30469
  • production: no

Culture and growth conditions

culture medium

  • @ref: 17476
  • name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/693
  • composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
17476positivegrowth37mesophilic
30469positivegrowth30-41
30469positiveoptimum37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17476microaerophile
30469facultative aerobe

spore formation

@refspore formationconfidence
30469no
69481no100
69480no99.998

observation

  • @ref: 30469
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3046923652dextrin+carbon source
3046917234glucose+carbon source
3046917306maltose+carbon source
3046937684mannose+carbon source
6837717634D-glucose+builds acid from
6837715824D-fructose+builds acid from
6837717306maltose+builds acid from
6837718257ornithine-degradation
6837727897tryptophan-energy source
6838129016arginine+hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6837735581indole-

enzymes

@refvalueactivityec
17476catalase+1.11.1.6
17476cytochrome-c oxidase+1.9.3.1
30469catalase+1.11.1.6
30469cytochrome oxidase+1.9.3.1
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
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase-3.2.1.23
68377lipase+
68377ornithine decarboxylase-4.1.1.17

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
17476++++--++-----
17476-++++--++----

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
17476+----+-----------+---+---------+/-

Isolation, sampling and environmental information

isolation

  • @ref: 17476
  • sample type: pharynx of a apparently healthy feral pigeon Columba livia f. domestica
  • host species: Columba livia f. domestica
  • geographic location: Lower Saxony, Hannover
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

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

Safety information

risk assessment

  • @ref: 17476
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17476
  • description: Riemerella columbipharyngis strain 8151 16S ribosomal RNA gene, partial sequence
  • accession: HQ286278
  • length: 1433
  • database: ena
  • NCBI tax ID: 1071918

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Riemerella columbipharyngis DSM 24015GCA_900101995scaffoldncbi1071918
66792Riemerella columbipharyngis strain DSM 240151071918.3wgspatric1071918
66792Riemerella columbipharyngis DSM 240152675903161draftimg1071918

GC content

@refGC-contentmethod
1747635.7high performance liquid chromatography (HPLC)
3046935.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.024yes
flagellatedno95.981no
gram-positiveno97.974no
anaerobicno97.468yes
aerobicno88.272yes
halophileno86.06no
spore-formingno97.671yes
glucose-fermentno84.051no
thermophileno98.069yes
glucose-utilyes78.389yes

External links

@ref: 17476

culture collection no.: DSM 24015, LMG 26094

straininfo link

  • @ref: 75117
  • straininfo: 371104

literature

  • topic: Phylogeny
  • Pubmed-ID: 22427448
  • title: Description of Riemerella columbipharyngis sp. nov., isolated from the pharynx of healthy domestic pigeons (Columba livia f. domestica), and emended descriptions of the genus Riemerella, Riemerella anatipestifer and Riemerella columbina.
  • authors: Rubbenstroth D, Ryll M, Hotzel H, Christensen H, Knobloch JK, Rautenschlein S, Bisgaard M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.036798-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Columbidae/*microbiology, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pharynx/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Riemerella/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17476Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24015)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24015
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
30469Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2680428776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
68377Automatically annotated from API NH
68381Automatically annotated from API rID32STR
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
75117Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371104.1StrainInfo: A central database for resolving microbial strain identifiers