Strain identifier

BacDive ID: 140303

Type strain: Yes

Species: Rodentibacter trehalosifermentans

Strain Designation: H1987082031

Strain history: <- H. Christensen, University of Copenhagen, Frederiksberg, DENMARK; H1987082031 <-W. Nicklas, German Cancer Research Centre, Heidelberg, Germany

NCBI tax ID(s): 1908263 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 42910

BacDive-ID: 140303

DSM-Number: 104075

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

description: Rodentibacter trehalosifermentans H1987082031 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from laboratory rat, trachea.

NCBI tax id

  • NCBI tax id: 1908263
  • Matching level: species

strain history

  • @ref: 42910
  • history: <- H. Christensen, University of Copenhagen, Frederiksberg, DENMARK; H1987082031 <-W. Nicklas, German Cancer Research Centre, Heidelberg, Germany

doi: 10.13145/bacdive140303.20230509.8.1

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

@ref: 42910

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter trehalosifermentans

full scientific name: Rodentibacter trehalosifermentans Adhikary et al. 2017

strain designation: H1987082031

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

@refnamegrowthlinkcomposition
43243Bovine blood agaryes
42910CHOCOLATE AGAR (DSMZ Medium 429b)yeshttps://mediadive.dsmz.de/medium/429bName: CHOCOLATE AGAR (DSMZ Medium 429b) Composition: Horse blood 100.0 g/l Sheep blood 100.0 g/l Columbia agar base
42910BHI/3 MEDIUM (DSMZ Medium 218)yeshttps://mediadive.dsmz.de/medium/218Name: BHI/3 MEDIUM (DSMZ Medium 218) Composition: Brain heart infusion 37.0 g/l Casein hydrolysate 10.0 g/l Starch 1.0 g/l Distilled water
42910COLUMBIA 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
63643positivegrowth37mesophilic
42910positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63643
  • oxygen tolerance: microaerophile

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4324313389nad+required for growth
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

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

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
42910laboratory rat, tracheaGermanyDEUEurope
43243rats samples
63643Laboratory rat,trachea

isolation source categories

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

Safety information

risk assessment

  • @ref: 42910
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42910
  • description: Rodentibacter trehalosifermentans strain H1987082031 16S ribosomal RNA gene, partial sequence
  • accession: KX858172
  • length: 1428
  • database: ena
  • NCBI tax ID: 1908263

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter trehalosifermentans H1987082031GCA_002000545contigncbi1908263
66792Rodentibacter trehalosifermentans H19870820312791354947draftimg1908263

GC content

@refGC-contentmethod
4324340.9
4291040.9sequence analysis

External links

@ref: 42910

culture collection no.: DSM 104075, CCUG 69668

straininfo link

  • @ref: 96608
  • straininfo: 407757

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
42910Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104075Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104075)
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
63643Curators of the CCUGhttps://www.ccug.se/strain?id=69668Culture Collection University of Gothenburg (CCUG) (CCUG 69668)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
96608Reimer, 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-ID407757.1