Strain identifier

BacDive ID: 140304

Type strain: Yes

Species: Rodentibacter rarus

Strain Designation: 2325/79

Strain history: <- H. Christensen, Veterinary Disease Biology, University of Copenhagen <- Institute of Avian Diseases, Langaa, Denmark

NCBI tax ID(s): 1908260 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 8.1 (current version)

General

@ref: 42911

BacDive-ID: 140304

DSM-Number: 103980

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

description: Rodentibacter rarus 2325/79 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from rat.

NCBI tax id

  • NCBI tax id: 1908260
  • Matching level: species

strain history

  • @ref: 42911
  • history: <- H. Christensen, Veterinary Disease Biology, University of Copenhagen <- Institute of Avian Diseases, Langaa, Denmark

doi: 10.13145/bacdive140304.20230509.8.1

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 rarus
  • full scientific name: Rodentibacter rarus Adhikary et al. 2017

@ref: 42911

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter rarus

full scientific name: Rodentibacter rarus Adhikary et al. 2017

strain designation: 2325/79

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43243negativeno
69480negative99.939

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

@refnamegrowthlinkcomposition
43243Bovine blood agaryes
43243Bovine blood agarno
42911COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
46562positivegrowth37mesophilic
42911positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 46562
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.991

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
4324323652dextrin+builds acid from
4324328053melibiose+builds acid from
4324316634raffinose-builds acid from
4324313389nad-required for growth
4324317108D-arabinose-builds acid from
4324318287L-fucose+builds acid from
4324317754glycerol+builds acid from

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
43243alpha-galactosidase+3.2.1.22

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
42911rat
43243rat samplesUSAUSAUSANorth America
46562MouseUSAUSANorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Muridae (Mouse/Rat)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2819.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_552;97_924;98_2186;99_2819&stattab=map
  • Last taxonomy: Rodentibacter rarus subclade
  • 16S sequence: AF024529
  • Sequence Identity:
  • Total samples: 787
  • soil counts: 2
  • aquatic counts: 9
  • animal counts: 775
  • plant counts: 1

Safety information

risk assessment

  • @ref: 42911
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42911
  • description: Rodentibacter rarus strain CCUG 17206 16S ribosomal RNA gene, complete sequence
  • accession: AF024529
  • length: 1480
  • database: ena
  • NCBI tax ID: 1908260

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter rarus CCUG 17206GCA_001998965contigncbi1908260
66792Rodentibacter rarus strain CCUG172061908260.3wgspatric1908260
66792Rodentibacter rarus CCUG172062791354952draftimg1908260

GC content

  • @ref: 43243
  • GC-content: 40.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.128no
gram-positiveno98.042yes
anaerobicno93.284no
aerobicno94.526yes
halophileno59.936no
spore-formingno98.812no
glucose-utilno51.839no
flagellatedno94.579yes
thermophileno98.923no
glucose-fermentyes55.043no

External links

@ref: 42911

culture collection no.: DSM 103980, CCUG 17206, HPA 41

straininfo link

  • @ref: 96609
  • straininfo: 51978

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
42911Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103980Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103980)
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
46562Curators of the CCUGhttps://www.ccug.se/strain?id=17206Culture Collection University of Gothenburg (CCUG) (CCUG 17206)
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96609Reimer, 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-ID51978.1