Strain identifier

BacDive ID: 140609

Type strain: Yes

Species: Rodentibacter heylii

Strain Designation: P309, C57

Strain history: <- CCUG; CCUG 998 <- K. Bövre, Natl. Vet. Inst., Oslo, Norway; C57

NCBI tax ID(s): 1906744 (species)

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: 67678

BacDive-ID: 140609

DSM-Number: 112292

keywords: genome sequence, Bacteria, mesophilic, Gram-negative, colony-forming

description: Rodentibacter heylii P309 is a mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from mouse.

NCBI tax id

  • NCBI tax id: 1906744
  • Matching level: species

strain history

  • @ref: 67678
  • history: <- CCUG; CCUG 998 <- K. Bövre, Natl. Vet. Inst., Oslo, Norway; C57

doi: 10.13145/bacdive140609.20230509.8.1

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

@ref: 67678

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter heylii

full scientific name: Rodentibacter heylii Adhikary et al. 2017

strain designation: P309, C57

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
43243MacConkey agarno
67678COLUMBIA 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

  • @ref: 67678
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4324317234glucose+fermentation
4324317632nitrate+reduction
4324316947citrate-carbon source
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
4324317924(-)-D-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
4324353426tween 80-hydrolysis
4324317108D-arabinose-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
4324318287L-fucose+builds acid from
4324316024D-mannose+builds acid from
4324317716lactose+/-builds acid from
4324317992sucrose+builds acid from
4324327082trehalose+builds acid from
4324323652dextrin-builds acid from
4324317634(-)-D-glucose+builds acid from
4324317754glycerol-builds acid from
4324328053melibiose+builds acid from
4324316634raffinose+builds acid from
6837717634D-glucose+builds acid from
6837716199urea+hydrolysis
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
6838116199urea+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
432438337porphyrinyes
4324315688acetoinno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4324317234glucose-
4324315688acetoin-
6838115688acetoin-

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
68381urease+3.5.1.5
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
68377gamma-glutamyltransferase+2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase+3.1.3.1
68377lipase-
68377urease+3.5.1.5
68377beta-lactamase-3.5.2.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
65643-+---+----++++-+----

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
67678-+-+/-+/--+-++-++
65643-++++++-++-+-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
65643--+-++------------+------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43243mouseAustraliaAustraliaAUSAustralia and Oceania
67678mouseAustraliaAUSAustralia and Oceania

isolation source categories

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

Safety information

risk assessment

  • @ref: 67678
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter heylii ATCC 12555GCA_001019715contigncbi1906744
66792[Pasteurella] pneumotropica strain ATCC 12555758.15wgspatric758
66792Rodentibacter heylii ATCC 125552651869757draftimg1906744

GC content

  • @ref: 43243
  • GC-content: 40.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno88.873yes
flagellatedno93.087no
gram-positiveno98.067yes
anaerobicno96.288no
aerobicno83.944no
halophileno52.086no
spore-formingno98.709no
glucose-utilno51.287no
thermophileno98.517no
glucose-fermentyes66.232no

External links

@ref: 67678

culture collection no.: MCCM 237, RGWyllie C57, HIM 1014-1, CCUG 998, ATCC 12555, DSM 112292

straininfo link

  • @ref: 96755
  • straininfo: 35605

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/urljournalpubmedcatalogue
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
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
65643Curators of the CCUGhttps://www.ccug.se/strain?id=998Culture Collection University of Gothenburg (CCUG) (CCUG 998)
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
67678Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-112292Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 112292)
68377Automatically annotated from API NH
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
96755Reimer, 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-ID35605.1