Strain identifier

BacDive ID: 133060

Type strain: Yes

Species: Citrobacter europaeus

Strain Designation: 97/79

Strain history: CIP <- 2000, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 97/79, Citrobacter freundii

NCBI tax ID(s): 1914243 (species)

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General

@ref: 24848

BacDive-ID: 133060

DSM-Number: 103031

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Citrobacter europaeus 97/79 is a facultative anaerobe, psychrophilic, Gram-negative human pathogen that was isolated from faeces from a human with diarrhoea.

NCBI tax id

  • NCBI tax id: 1914243
  • Matching level: species

strain history

@refhistory
422142000, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 97/79, Citrobacter freundii
24848<- CIP <- P. A. D. Grimont, Institut Pasteur, Paris, France
119144CIP <- 2000, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 97/79, Citrobacter freundii

doi: 10.13145/bacdive133060.20230509.8.1

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 europaeus
  • full scientific name: Citrobacter europaeus Ribeiro et al. 2017

@ref: 24848

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter europaeus

full scientific name: Citrobacter europaeus Ribeiro et al. 2017

strain designation: 97/79

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25143negative4-5 µm1-2 µmrod-shapedyes
69480yes96.766
69480negative99.99
119144negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25143trypticase soy broth (TSB; Sigma-Aldrich)yes
42214MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
24848TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
24848COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
119144CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119144CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
25143positivegrowth20psychrophilic
25143positivegrowth25mesophilic
25143positivegrowth30mesophilic
25143positivegrowth37mesophilic
25143positivegrowth50thermophilic
42214positivegrowth30mesophilic
24848positivegrowth28mesophilic
119144positivegrowth5-41

culture pH

  • @ref: 25143
  • ability: positive
  • type: growth
  • pH: 5.0-10.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25143facultative anaerobe
119144facultative anaerobe

spore formation

@refspore formationconfidence
25143no
69481no100
69480no99.937

halophily

  • @ref: 25143
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-15 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
251433-O-methyl alpha-D-glucopyranoside-builds acid from
25143amygdalin-builds acid from27613
25143citrate-carbon source16947
25143ribitol-builds acid from15963
25143D-arabitol-builds acid from18333
25143D-fucose-builds acid from28847
25143D-lyxose-builds acid from62318
25143melezitose-builds acid from6731
25143D-tagatose-builds acid from16443
25143turanose-builds acid from32528
25143erythritol-builds acid from17113
25143esculin ferric citrate-builds acid from
25143gelatin-degradation5291
25143glycogen-builds acid from28087
25143inulin-builds acid from15443
25143L-arabitol-builds acid from18403
25143L-arginine-assimilation16467
25143L-lysine-assimilation18019
25143L-tryptophan-assimilation16828
25143L-xylose-builds acid from65328
25143methyl alpha-D-mannoside-builds acid from43943
25143methyl beta-D-xylopyranoside-builds acid from74863
25143starch-builds acid from28017
25143sucrose-builds acid from17992
25143tryptophan-energy source27897
25143xylitol-builds acid from17151
251432-dehydro-D-gluconate+builds acid from16808
251435-dehydro-D-gluconate+builds acid from58143
25143arbutin+builds acid from18305
25143cellobiose+builds acid from17057
25143D-arabinose+builds acid from17108
25143D-fructose+builds acid from15824
25143D-galactose+builds acid from12936
25143D-glucose+builds acid from17634
25143D-mannitol+builds acid from16899
25143D-mannose+builds acid from16024
25143D-ribose+builds acid from16988
25143D-sorbitol+builds acid from17924
25143D-xylose+builds acid from65327
25143galactitol+builds acid from16813
25143gentiobiose+builds acid from28066
25143glucose+fermentation17234
25143glycerol+builds acid from17754
25143myo-inositol+builds acid from17268
25143L-arabinose+builds acid from30849
25143L-fucose+builds acid from18287
25143L-rhamnose+builds acid from62345
25143L-sorbose+builds acid from17266
25143lactose+builds acid from17716
25143maltose+builds acid from17306
25143melibiose+builds acid from28053
25143N-acetylglucosamine+builds acid from506227
25143nitrate+reduction17632
25143O-nitrophenyl-beta-D-galactopyranosid+builds acid from
25143potassium gluconate+builds acid from32032
25143raffinose+builds acid from16634
25143salicin+builds acid from17814
25143trehalose+builds acid from27082
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol+builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose+builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
119144mannitol+fermentation29864
119144citrate+carbon source16947
119144glucose+fermentation17234
119144lactose-fermentation17716
119144nitrate+reduction17632
119144nitrite+reduction16301
119144malonate-assimilation15792
119144sodium thiosulfate+builds gas from132112
119144glucose+degradation17234

antibiotic resistance

  • @ref: 119144
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2514315688acetoinno
2514317997dinitrogenno
2514335581indoleno
2514316136hydrogen sulfideyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes
11914435581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
2514317234glucose+
2514315688acetoin-
2514335581indole-
6836815688acetoin-
6836835581indole-
11914415688acetoin-
11914417234glucose+

enzymes

@refvalueactivityec
25143catalase+1.11.1.6
25143cytochrome oxidase-1.9.3.1
25143tryptophan deaminase-4.1.99.1
25143urease-3.5.1.5
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
119144oxidase-
119144beta-galactosidase+3.2.1.23
119144alcohol dehydrogenase+1.1.1.1
119144gelatinase-
119144catalase+1.11.1.6
119144lysine decarboxylase-4.1.1.18
119144ornithine decarboxylase-4.1.1.17
119144phenylalanine ammonia-lyase-4.3.1.24
119144tryptophan deaminase-
119144urease-3.5.1.5
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
119144-+---++++-++++-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
24848++--++-----++-++-+++-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
24848-+-++++---++++++++++--+--++++++-+--+--------+--+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119144+++++++-++++++++++-+++-++----+-+++--+--+--++++-++++-++++++-++----+-------+-+---++-+++-+-+++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
25143faeces from a human with diarrhoeaUSAUSANorth America
24848faeces from a human with diarrhoea
119144Human, FecesFranceFRAEuropeSaint Paul, Réunion Island1979-11-14

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
24848yes, in single cases1Risk group (German classification)
1191441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24848
  • description: Citrobacter europaeus genomic DNA containing 16S region, strain 97/79 (=CIP 106467)
  • accession: LT615140
  • length: 1336
  • database: ena
  • NCBI tax ID: 1914243

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter europaeus 97/79GCA_900079995contigncbi1914243
66792Citrobacter europaeus strain FDAARGOS_14901914243.13completepatric1914243
66792Citrobacter freundii CIP1064672906139326draftimg546
66792Citrobacter europaeus strain FDAARGOS_14901914243.21completepatric1914243
66792Citrobacter europaeus strain FDAARGOS_14901914243.15completepatric1914243
66792Citrobacter europaeus strain FDAARGOS_14901914243.18completepatric1914243

GC content

@refGC-content
2514352
2484852.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.396yes
gram-positiveno98.166yes
anaerobicno93.192yes
aerobicyes54.694yes
halophileno91.173no
spore-formingno93.713yes
glucose-utilyes93.851no
flagellatedyes52.459no
thermophileno99.406no
glucose-fermentyes91.869yes

External links

@ref: 24848

culture collection no.: DSM 103031, CIP 106467

straininfo link

  • @ref: 91326
  • straininfo: 67879

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902229
  • title: Citrobacter europaeus sp. nov., isolated from water and human faecal samples.
  • authors: Ribeiro TG, Clermont D, Branquinho R, Machado E, Peixe L, Brisse S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001606
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Citrobacter/classification, DNA, Bacterial/genetics, Europe, Feces/*microbiology, Genes, Bacterial, Humans, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology
  • topic2: Pathogenicity

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
24848Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103031Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103031)
25143T. G. C. Ribeiro, D.,Branquinho, R.,Machado, E.,Peixe, L.,Brisse, S.Citrobacter europaeus sp. nov., isolated from water and human faecal samples10.1099/ijsem.0.001606IJSEM 67: 170-173 201727902229
42214Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18601
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
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91326Reimer, 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-ID67879.1
119144Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106467Collection of Institut Pasteur (CIP 106467)