Citrobacter farmeri

Bacteria
General | Carbohydrate O/F | Substrate utilisation | Enzymes | Metabolites | Antibiotics

Overview

  • Citrobacter farmeri is a Gram-negative, non-spore-forming, facultatively anaerobic, motile, rod-shaped bacterium. It has been detected in at least 3 gut microbiome compilation studies or metastudies. Citrobacter farmeri is probably a common, although minor, coloniser of the gut. (Brenner1993; Brenner1999; Friederiksen2005Bergey)



  • This organism has been recovered from human faeces, urine, and clinical sources. The risk classification (www.baua.de) for this organism is 2, i.e., risk of individual infection, but low risk of spread. Could be a possible pathogen in humans, but unknown at this stage. A possible gut commensal.
    • QUIRKS
  • In 14% of Europeans (unseenbio.com). Minor coloniser.
    • GENERAL CHARACTERISTICS (Brenner1993); (Brenner1999); (Friederiksen2005Bergey);
    Character Response
  • Substrates hydrolysed or digested:
  • arginine;
  • H+
  • Acid from carbohydrates usually produced:
  • arabinose; L-arabinose; glucose; mannose; rhamnose; xylose; amygdalin; cellubiose; maltose; mucate; melibiose; raffinose; sucrose; trehalose; glycerol; mannitol; sorbitol; 5-ketogluconate; α-methyl glucoside;
  • ⥅
  • Substrates assimilated or utilised:
  • N-acetylglucosamine; L-arabinose; cellubiose; fructose; fucose; galactose; gluconate; gentiobiose; glucose; glycerol; lactose; maltose; maltotriose; mannitol; mannose; melibiose; methyl-α-glucoside; rhamnose; ribose; raffinose; sorbitol; sorbose; sucrose; trehalose; xylose; alanine; D-alanine; aspartate; glutamate; proline; serine; acetate; benzoate; citrate; fumarate; DL-glycerate; 3-hydroxybenzoate; 4-hydroxybenzoate; 2-ketogluconate; 5-ketogluconate; DL-lactate; malate; L-malate; mucate; propionate; saccharate; succinate; methyl-β-glucoside; methyl-α-galactoside; maltitol; palatinose; glutamine; D-glucuronate; gentisate; tricarballylate;
  • ±
  • Strain-dependent substrate utilisation:
  • D-tagatose; δ-aminovalerate; aconitate; 2-ketoglutarate; L-tartrate; methyl-β-galactoside;
  • Active enzymes:
  • arginine dihydrolase; catalase; α-galactosidase; β-galactosidase; β-glucosidase; ornithine decarboxylase;
  • ±
  • Strain-dependent active enzymes:
  • urease;
    • SPECIAL FEATURES (Brenner1993); (Brenner1999); (Friederiksen2005Bergey);
    Character Response
  • ✓
  • Metabolites produced:
  • indole;
  • ✗
  • Metabolites not produced:
  • H₂S;
  • ✓
  • Methyl red test:
  • active
  • ✓
  • VP test:
  • active
  • ✓
  • ONPG test:
  • active
  • KCN growth:
  • growth observed
  • ✓
  • NO3➔NO2:
  • reduced
  • ✗
  • Pigments:
  • not produced
    • RESPONSE TO ANTIBIOTICS (Friederiksen2005Bergey);
    Class Active Resistant
  • Penicillins:
  • ertapenem; imipenem;
  • ampicillin; aztreonam; ticarcillin;
  • Cephalosporins:
  • cefepime;
  • ceftazidime; cefuroxime;
  • Macrolides:
  • erythromycin;
  • Tetracyclines:
  • tetracycline;
  • Quinolines:
  • ciprofloxacin; gatifloxacin; nalidixic-acid;
  • Heterocycles:
  • chloramphenicol; fosfomycin; nitrofurantoin; trimethoprim;
  • fusidic-acid;
  • Vancomycins:
  • vancomycin;
  • Miscellaneous antibiotics:
  • polymyxin B;
  • clindamycin; lincomycin;

  • Brenner, D. J., Grimont, P. A., Steigerwalt, A. G., Fanning, G. R., Ageron, E., & Riddle, C. F. (1993). Classification of citrobacteria by DNA hybridization: designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and three unnamed Citrobacter genomospecies. International Journal of Systematic Bacteriology, 43(4), 645–658.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Proteobacteria Class:  Gammaproteobacteria Order:  Enterobacterales Family:  Enterobacteriaceae Genus:  Citrobacter Gram stain:  neg O2 Relation.:  facultatively anaerobic Spore:  No spore Motility:  Swimming Morphology:  Rod Pigment:  neg
    Health:  Unknown
    Source:  human faeces, urine, and clinical sources
    		Aesculin:  neg Urea:  neg Gelatin:  neg Arginine:  + DNA:  neg
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Arabinose:  + L-Arabinose:  + Glucose:  + Mannose:  + Rhamnose:  + Xylose:  + Cellubiose:  + Lactose:  neg Maltose:  + Melezitose:  neg Melibiose:  + Sucrose:  + Trehalose:  + Amygdalin:  + Aesculin:  neg Adonitol:  neg D-Arabitol:  neg L-Arabitol:  neg Dulcitol:  neg Erythritol:  neg Glycerol:  d(+) Inositol:  neg Mannitol:  + Sorbitol:  + 5-Ketogluconate:  + Me-α-D-Glc:  + Salicin:  neg
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    L-Arabinose:  + Fructose:  + Fucose:  + Galactose:  + Glucose:  + D-Lyxose:  neg Mannose:  + Rhamnose:  + Ribose:  + Sorbose:  + D-Tagatose:  d Xylose:  + Cellubiose:  + Gentiobiose:  + Lactose:  + Maltose:  + Maltotriose:  + Melezitose:  neg Melibiose:  + Raffinose:  + Sucrose:  + Trehalose:  + N_Acetyl_glucosamine:  + Adonitol:  neg D-Arabitol:  neg L-Arabitol:  neg Dulcitol:  neg Erythritol:  neg Aesculin:  neg Ethanolamine:  neg Gluconate:  + Glycerol:  + Inositol:  neg Mannitol:  + Me-α-D-Glc:  + Sorbitol:  + Xylitol:  neg Ala:  + D-Ala:  + 4-Aminobutyrate:  neg 5-Aminovalerate:  d(neg) Asp:  + Betaine:  neg Glu:  + Histamine:  neg His:  neg Pro:  d(+) Ser:  + Trigonelline:  neg Tryptamine:  neg Trp:  neg Tyr:  neg Acetate:  d(+) Aconitate:  d Benzoate:  + Caprate:  neg Caprylate:  neg Citrate:  + Fumarate:  + Glutarate:  neg DL-Glycerate:  + 3-Hydroxybutyrate:  neg 3-Hydroxybenzoate:  + 4-Hydroxybenzoate:  + Itaconate:  neg 2-Ketogluconate:  + 5-Ketogluconate:  + DL-Lactate:  + Malate:  + L-Malate:  + Malonate:  neg Mucate:  + Phenylacetate:  neg Phenylpropionate:  neg Propionate:  + Quinate:  neg Saccharate:  + Succinate:  + D-Tartrate:  neg L-Tartrate:  d
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Oxidase:  neg Catalase:  + Urease:  d Ac-β-glcamnd:  neg α-Galactosidase:  + β-Galactosidase:  + α-Glucosidase:  neg β-Glucosidase:  + β-Glucuronidase:  neg ArgDH:  + LysDC:  neg OrnDC:  + Phe deaminase:  neg DNAse:  neg Lipase:  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		H2S:  neg Indole:  + Pigment:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    ampicillin:  Res
    aztreonam:  Var(MIC50): >0.12, MIC90: >16, R(4->64)
    ticarcillin:  Res
    ertapenem:  S(MIC50): 0.008, MIC90: 0.25, RNG: (0.008-4)
    imipenem:  S(MIC50): 0.25, MIC90: 1, RNG: (0.5->8)
    cefepime:  S(MIC50): 0.12, MIC90: 0.5, RNG: (0.12->16)
    cefotaxime:  RNG: (1-32)
    cefpodoxime:  RNG: (1->16)
    ceftazidime:  R(MIC50): >2, MIC90: >16, RNG: (2->16)
    cefuroxime:  R(8)
    amikacin:  Var(MIC50): 1, MIC90: 2, RNG: (0.25-32)
    gentamicin:  Var(MIC50): 2, MIC90: 2, RNG: (2->16)
    erythromycin:  Res
    ciprofloxacin:  S(MIC50): 0.03, MIC90: 1, RNG: (0.008->16)
    gatifloxacin:  S(MIC50): 0.03, MIC90: 1, RNG: (0.03->4)
    nalidixic-acid:  Sens
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    tetracycline:  Sens
    vancomycin:  Res
    chloramphenicol:  Sens
    fosfomycin:  Sens
    nitrofurantoin:  Sens
    trimethoprim:  Sens
    clindamycin:  Res
    lincomycin:  Res
    polymyxin_B:  Sens
    fusidic-acid:  Res

    References

    SPECIFIC REFERENCES FOR CITROBACTER FARMERI
  • Brenner1993 - Classification of Citrobacteria by DNA Hybridization: Designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and Three Unnamed Citrobacter Genomospecies.
  • Brenner1999 - Biochemical identification of Citrobacter species defined by DNA hybridization and description of Citrobacter gillenii sp. nov. (formerly Citrobacter genomospecies 10) and Citrobacter murliniae sp. nov. (formerly Citrobacter genomospecies 11).
  • Friederiksen2005Bergey - Bergey's manual of systematic bacteriology. Vol. 2, The Gammaproteobacteria Part B. Family Enterobacteriaceae, Genus X. Citrobacter
  • Weir2013 - Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR CITROBACTER FARMERI
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • ...............................
    • GENERAL REFERENCES FOR CITROBACTER FARMERI
  • CCUG - Culture Collection University of Gothenburg - Entire Collection
    • Added: April 08, 2021