Strain identifier

BacDive ID: 4344

Type strain: Yes

Species: Citrobacter farmeri

Strain Designation: E 3020, 2991-81

Strain history: CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 2991-81 <- New-York State Hlth. Dept.: strain E 3020

NCBI tax ID(s): 67824 (species)

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General

@ref: 7108

BacDive-ID: 4344

DSM-Number: 17655

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Citrobacter farmeri E 3020 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 67824
  • Matching level: species

strain history

@refhistory
7108<- CIP <- P. A. D. Grimont, IP <- CDC <- New York State Health Department
119285CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 2991-81 <- New-York State Hlth. Dept.: strain E 3020

doi: 10.13145/bacdive4344.20230509.8.1

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 farmeri
  • full scientific name: Citrobacter farmeri Brenner et al. 1993

@ref: 7108

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter farmeri

full scientific name: Citrobacter farmeri Brenner et al. 1993

strain designation: E 3020, 2991-81

type strain: yes

Morphology

cell morphology

  • @ref: 119285
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7108NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39040MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119285CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7108positivegrowth30mesophilic
39040positivegrowth30
50278positivegrowth37
119285positivegrowth10-41
119285nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 50278
  • oxygen tolerance: aerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
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
119285citrate-carbon source16947
119285glucose+fermentation17234
119285lactose-fermentation17716
119285nitrate+reduction17632
119285nitrite+reduction16301
119285malonate-assimilation15792
119285sodium thiosulfate-builds gas from132112

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
11928535581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole+
11928515688acetoin-
11928517234glucose-

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
119285oxidase-
119285beta-galactosidase+3.2.1.23
119285alcohol dehydrogenase-1.1.1.1
119285gelatinase-
119285catalase+1.11.1.6
119285lysine decarboxylase-4.1.1.18
119285ornithine decarboxylase+4.1.1.17
119285tryptophan deaminase-
119285urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119285-+++-+----++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7108++-++---++-++-++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119285+-++++---++++++--++-++-+/-+/-+/-+++/-+++--+---++-+-+--+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119285+++++++++++---++++-++++++-----++-++++-----+++---+++-++++++-++-++-+++-------+---++-----+--+--++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7108human faecesNew YorkUSAUSANorth America
50278Human feces
119285Human, FecesNew YorkUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_363.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_307;99_363&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: AF025371
  • Sequence Identity:
  • Total samples: 2518
  • soil counts: 59
  • aquatic counts: 191
  • animal counts: 2129
  • plant counts: 139

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71082Risk group (German classification)
1192851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7108
  • description: Citrobacter farmeri 16S ribosomal RNA gene, partial sequence
  • accession: AF025371
  • length: 1511
  • database: ena
  • NCBI tax ID: 67824

Genome sequences

  • @ref: 66792
  • description: Citrobacter farmeri strain FDAARGOS 1423
  • accession: 67824.35
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 67824

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.495no
anaerobicno95.114no
halophileno92.373no
spore-formingno94.329no
glucose-utilyes96.195no
thermophileno99.384no
flagellatedyes52.34no
motileyes88.055no
aerobicyes78.16no
glucose-fermentyes92.984no

External links

@ref: 7108

culture collection no.: DSM 17655, ATCC 51112, CDC 2991-81, CIP 104553, CCUG 30798

straininfo link

  • @ref: 73835
  • straininfo: 42808

literature

  • topic: Phylogeny
  • Pubmed-ID: 30079059
  • title: Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum beta-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces.
  • authors: Potter RF, D'Souza AW, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD, Dantas G
  • journal: Front Microbiol
  • DOI: 10.3389/fmicb.2018.01629
  • year: 2018

Reference

@idauthorscataloguedoi/urltitle
7108Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17655)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17655
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
39040Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16474
50278Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30798)https://www.ccug.se/strain?id=30798
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
73835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42808.1StrainInfo: A central database for resolving microbial strain identifiers
119285Curators of the CIPCollection of Institut Pasteur (CIP 104553)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104553