Strain identifier

BacDive ID: 4340

Type strain: Yes

Species: Citrobacter rodentium

Strain Designation: DO 14784

Strain history: CIP <- 1996, ATCC <- CDC: strain 1843-73, Citrobacter sp. <- CT. Hlth. Dept.: strain DO 14784

NCBI tax ID(s): 1218085 (strain), 67825 (species)

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General

@ref: 6539

BacDive-ID: 4340

DSM-Number: 16636

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped, animal pathogen

description: Citrobacter rodentium DO 14784 is a mesophilic, Gram-negative, rod-shaped animal pathogen that was isolated from hamster.

NCBI tax id

NCBI tax idMatching level
67825species
1218085strain

strain history

@refhistory
6539<- ATCC <- C. F. Riddle <- Connecticut State Health Dept.
67770CCUG 30795 <-- R. E. Weaver CDC 1843-73 <-- Connecticut State Health Dept., USA, DO 14784.
122246CIP <- 1996, ATCC <- CDC: strain 1843-73, Citrobacter sp. <- CT. Hlth. Dept.: strain DO 14784

doi: 10.13145/bacdive4340.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Citrobacter
  • species: Citrobacter rodentium
  • full scientific name: Citrobacter rodentium Schauer et al. 1996

@ref: 6539

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter rodentium

full scientific name: Citrobacter rodentium Schauer et al. 1996

strain designation: DO 14784

type strain: yes

Morphology

cell morphology

  • @ref: 122246
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6539CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38514MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122246CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122246CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6539positivegrowth37mesophilic
38514positivegrowth30mesophilic
50275positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122246-+++-++-+-++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6539+--+-----+-++-++--++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122246+++++----+++-+-+---+++-+-------+-+--+------++--+++--+++++--++----++-----+------++-+---+--+-++++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6539hamsterConnecticutUSAUSANorth America
50275Mouse
67770HamsterCTUSAUSANorth America
122246Animal, HamsterConnecticutUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Rodentia (Other)

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6539yes2Risk group (German classification)
1222461Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter rodentium 16S ribosomal RNA gene, partial sequenceAF0253631496ena67825
67770Citrobacter rodentium gene for 16S rRNA, partial sequence, strain: NBRC 105723AB6822871467ena67825
67770Citrobacter rodentium strain CIP 104675 16S ribosomal RNA gene, partial sequenceKM5159721467ena67825

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter rodentium NBRC 1057231218085.3wgspatric1218085
66792Citrobacter rodentium NBRC 1057232600255055draftimg1218085
67770Citrobacter rodentium NBRC 105723 = DSM 16636GCA_000759815contigncbi1218085
66792Citrobacter rodentium ATCC 51116GCA_015965415contigncbi67825
66792Citrobacter rodentium NBRC 105723 = DSM 16636GCA_015965555contigncbi1218085
66792Citrobacter rodentium NBRC 105723 = DSM 16636GCA_021278985completencbi1218085

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno54.431no
gram-positiveno98.054no
anaerobicno93.948no
aerobicyes83.808no
halophileno91.271no
spore-formingno93.638no
motileyes84.53no
glucose-fermentyes93.184yes
thermophileno99.33yes
glucose-utilyes96.071no

External links

@ref: 6539

culture collection no.: DSM 16636, ATCC 51116, CDC 1843-73, CIP 104675, CCUG 30795, JCM 14073, CCM 7398, NBRC 105723

straininfo link

  • @ref: 73832
  • straininfo: 46897

literature

topicPubmed-IDtitleauthorsjournalDOIyear
Phylogeny30079059Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum beta-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces.Potter RF, D'Souza AW, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD, Dantas GFront Microbiol10.3389/fmicb.2018.016292018
Genetics35380454Complete Genome Sequence of the Type Strain Citrobacter rodentium DSM 16636.Wahl A, Neuhaus KMicrobiol Resour Announc10.1128/mra.01237-212022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6539Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16636)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16636
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38514Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16609
50275Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30795)https://www.ccug.se/strain?id=30795
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
73832Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46897.1StrainInfo: A central database for resolving microbial strain identifiers
122246Curators of the CIPCollection of Institut Pasteur (CIP 104675)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104675