Strain identifier

BacDive ID: 140301

Type strain: Yes

Species: Rodentibacter ratti

Strain Designation: F75

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

NCBI tax ID(s): 1906745 (species)

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General

@ref: 42908

BacDive-ID: 140301

DSM-Number: 103977

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

description: Rodentibacter ratti F75 is a microaerophile, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from chicken, respiratory tract.

NCBI tax id

  • NCBI tax id: 1906745
  • Matching level: species

strain history

  • @ref: 42908
  • history: <- H. Christensen, Veterinary Disease Biology, University of Copenhagen, Denmark <- M. Bisgaard, Institute of Avian Diseases, Langaa, Denmark

doi: 10.13145/bacdive140301.20230509.8.1

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

@ref: 42908

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Rodentibacter

species: Rodentibacter ratti

full scientific name: Rodentibacter ratti Adhikary et al. 2017

strain designation: F75

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
43243MacConkey agaryes
43243Bovine blood agaryes
42908COLUMBIA 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
63640positivegrowth37mesophilic
42908positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63640
  • 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
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
4324317754glycerol+builds acid from
4324328053melibiose-builds acid from
4324316634raffinose-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836917632nitrate+reduction

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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
42908++/---+--+------------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
42908chicken, respiratory tractDenmarkDNKEurope
43243chicken samplesDenmarkDNKEuropeDenmark
63640ChickenDenmarkDNKEurope

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_1565.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_552;97_924;98_1235;99_1565&stattab=map
  • Last taxonomy: Rodentibacter ratti
  • 16S sequence: AY172726
  • Sequence Identity:
  • Total samples: 208
  • aquatic counts: 5
  • animal counts: 203

Sequence information

16S sequences

  • @ref: 42908
  • description: Rodentibacter ratti strain F75 16S ribosomal RNA gene, partial sequence
  • accession: AY172726
  • length: 1451
  • database: ena
  • NCBI tax ID: 1906745

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rodentibacter ratti F75GCA_002000485contigncbi1906745
66792Rodentibacter ratti F752788500311draftimg1906745

GC content

@refGC-contentmethod
4324340.2
4290840.2sequence analysis

External links

@ref: 42908

culture collection no.: DSM 103977, CCUG 69665

straininfo link

  • @ref: 96606
  • straininfo: 400364

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
42908Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103977Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103977)
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
63640Curators of the CCUGhttps://www.ccug.se/strain?id=69665Culture Collection University of Gothenburg (CCUG) (CCUG 69665)
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
68369Automatically annotated from API 20NE
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/
96606Reimer, 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-ID400364.1