Strain identifier

BacDive ID: 140305

Type strain: Yes

Species: Rodentibacter mrazii

Strain Designation: Ppn418

Strain history: <- H. Christensen, University of Copenhagen, Veterinary Disease Biology, Denmark <- R. Boot, Laboratory for Infectious Disease and Screening, Bilthoven, Netherlands

NCBI tax ID(s): 1908257 (species)

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General

@ref: 42912

BacDive-ID: 140305

DSM-Number: 103979

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

description: Rodentibacter mrazii Ppn418 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from nasopharynx of wood mouse Apodemus sylvaticus.

NCBI tax id

  • NCBI tax id: 1908257
  • Matching level: species

strain history

  • @ref: 42912
  • history: <- H. Christensen, University of Copenhagen, Veterinary Disease Biology, Denmark <- R. Boot, Laboratory for Infectious Disease and Screening, Bilthoven, Netherlands

doi: 10.13145/bacdive140305.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Rodentibacter
  • species: Rodentibacter mrazii
  • full scientific name: Rodentibacter mrazii Adhikary et al. 2017

@ref: 42912

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter mrazii

full scientific name: Rodentibacter mrazii Adhikary et al. 2017

strain designation: Ppn418

type strain: yes

Morphology

cell morphology

  • @ref: 43243
  • gram stain: negative
  • motility: no

colony morphology

  • @ref: 43243
  • type of hemolysis: gamma
  • colony size: 1-2 mm
  • colony shape: circular
  • incubation period: 1 day
  • medium used: Bovine blood agar

Culture and growth conditions

culture medium

  • @ref: 42912
  • 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
63644positivegrowth37mesophilic
42912positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63644
  • oxygen tolerance: microaerophile

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4324317234glucose-fermentation
4324316537galactarate+builds acid from
4324315792malonate+builds base from
4324315226tetrathionate-reduction
4324353424tween 20-hydrolysis
4324348095(-)-D-fructose+builds acid from
4324312936D-galactose+builds acid from
4324317306maltose+builds acid from
4324317634(+)-D-glucose+builds acid from
4324348095(-)-D-fructose-builds gas from
4324312936D-galactose-builds gas from
4324317306maltose-builds gas from
4324317634(+)-D-glucose-builds gas from
4324317113erythritol-builds acid from
4324315963ribitol-builds acid from
4324317151xylitol-builds acid from
4324318333(+)-D-arabitol-builds acid from
4324365328(-)-L-xylose-builds acid from
4324316813galactitol-builds acid from
4324317924D-sorbitol+builds acid from
4324328847(+)-D-fucose-builds acid from
4324362345L-rhamnose-builds acid from
4324317266(-)-L-sorbose-builds acid from
4324317057cellobiose-builds acid from
432436731melezitose-builds acid from
43243(+)-D-glycogen-builds acid from
4324315443inulin-builds acid from
432434853esculin-builds acid from
4324327613amygdalin-builds acid from
4324318305arbutin-builds acid from
4324328066gentiobiose-builds acid from
4324317814salicin-builds acid from
4324332528turanose-builds acid from
4324330849L-arabinose-builds acid from
4324316988(-)-D-ribose+builds acid from
4324365327D-xylose+builds acid from
4324317268myo-inositol+builds acid from
4324316899D-mannitol-builds acid from
4324316024D-mannose+builds acid from
4324317716lactose+builds acid from
4324317992sucrose+builds acid from
4324327082trehalose+builds acid from
4324328053melibiose+builds acid from
4324316634raffinose+builds acid from
4324313389nad-required for growth

metabolite production

  • @ref: 43243
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4324317234glucose-
4324315688acetoin-

enzymes

@refvalueactivityec
43243catalase+1.11.1.6
43243cytochrome oxidase+1.9.3.1
43243urease+3.5.1.5
43243alkaline phosphatase+3.1.3.1
43243arginine dihydrolase-3.5.3.6
43243phenylalanine deaminase-4.3.1.5
43243gelatinase-
43243beta-glucosidase-3.2.1.21
43243alpha-fucosidase-3.2.1.51
43243beta-xylosidase-
43243alpha-mannosidase-3.2.1.24
43243lysine decarboxylase-4.1.1.18
43243ornithine decarboxylase+4.1.1.17
43243beta-galactosidase+3.2.1.23
43243alpha-glucosidase+3.2.1.20
43243beta-glucuronidase+/-3.2.1.31

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
42912nasopharynx of wood mouse Apodemus sylvaticusApodemus sylvaticusNetherlandsNLDEurope
43243sample from Apodemus silvaticus
63644Apodemus sylvaticus,nasopharynx,rodentNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_2695.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_552;97_924;98_1235;99_2695&stattab=map
  • Last taxonomy: Rodentibacter mrazii
  • 16S sequence: KX858294
  • Sequence Identity:
  • Total samples: 109
  • aquatic counts: 2
  • animal counts: 107

Safety information

risk assessment

  • @ref: 42912
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42912
  • description: Rodentibacter mrazii strain Ppn418 16S ribosomal RNA gene, partial sequence
  • accession: KX858294
  • length: 1357
  • database: ena
  • NCBI tax ID: 1908257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter mrazii Ppn418GCA_001998825contigncbi1908257
66792Rodentibacter mrazii ppn4182791354949draftimg1908257

GC content

@refGC-contentmethod
4324340
4291240.0sequence analysis

External links

@ref: 42912

culture collection no.: DSM 103979, CCUG 69669

straininfo link

  • @ref: 96610
  • straininfo: 400811

literature

  • topic: Phylogeny
  • Pubmed-ID: 28629498
  • title: Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies.
  • authors: Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbaek B, Korczak B, Christensen H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001866
  • year: 2017
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, Pasteurellaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42912Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103979Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103979)
43243Sadhana Adhikary, Werner Nicklas, Magne Bisgaard, Ron Boot, Peter Kuhnert, Torsten Waberschek, Bent Aalbaek, Bozena Korczak and Henrik ChristensenRodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies10.1099/ijsem.0.001866IJSEM 67: 1793-1806 201728629498
63644Curators of the CCUGhttps://www.ccug.se/strain?id=69669Culture Collection University of Gothenburg (CCUG) (CCUG 69669)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96610Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400811.1