Strain identifier

BacDive ID: 140302

Type strain: Yes

Species: Rodentibacter heidelbergensis

Strain Designation: 996025094, Ac69

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

NCBI tax ID(s): 1908258 (species)

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General

@ref: 42909

BacDive-ID: 140302

DSM-Number: 103978

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

description: Rodentibacter heidelbergensis 996025094 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from rat, lung.

NCBI tax id

  • NCBI tax id: 1908258
  • Matching level: species

strain history

  • @ref: 42909
  • history: <- H. Christensen, University of Copenhagen,Veterinary Disease Biology <- R. Boot, Laboratory for Infectious Disease and Screening, Bilthoven, Netherlands <- W. Nicklas

doi: 10.13145/bacdive140302.20230509.8.1

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

@ref: 42909

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter heidelbergensis

full scientific name: Rodentibacter heidelbergensis Adhikary et al. 2017

strain designation: 996025094, Ac69

type strain: yes

Morphology

cell morphology

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

colony morphology

@reftype of hemolysiscolony sizecolony shapeincubation periodmedium used
43243gamma1-2 mmcircular1 dayBovine blood agar
636421 day

pigmentation

  • @ref: 43243
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43243Bovine blood agaryes
43243MacConkey agarno
42909COLUMBIA 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
63642positivegrowth37mesophilic
42909positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63642
  • 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
4324323652dextrin+builds acid from
4324328053melibiose-builds acid from
4324316634raffinose+builds acid from
4324353426tween 80-hydrolysis

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 typecountryorigin.countrycontinent
42909rat, lungGermanyDEUEurope
43243rats samples
63642Rat,lungNetherlandsNLDEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7335.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_552;97_924;98_2091;99_7335&stattab=map
  • Last taxonomy: Rodentibacter heidelbergensis
  • 16S sequence: KX858081
  • Sequence Identity:
  • Total samples: 93
  • aquatic counts: 1
  • animal counts: 92

Safety information

risk assessment

  • @ref: 42909
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42909
  • description: Rodentibacter heidelbergensis strain 1996025094 16S ribosomal RNA gene, partial sequence
  • accession: KX858081
  • length: 1510
  • database: ena
  • NCBI tax ID: 1908258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter heidelbergensis Ac69GCA_002000125contigncbi1908258
66792Rodentibacter heidelbergensis Ac692788500309draftimg1908258

GC content

@refGC-contentmethod
4324340.4
4290940.4sequence analysis

External links

@ref: 42909

culture collection no.: DSM 103978, CCUG 69667

straininfo link

  • @ref: 96607
  • straininfo: 400849

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
42909Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103978Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103978)
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
63642Curators of the CCUGhttps://www.ccug.se/strain?id=69667Culture Collection University of Gothenburg (CCUG) (CCUG 69667)
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/
96607Reimer, 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-ID400849.1