Table 1

Target bacterial groups, primer sequences, conventional PCR conditions, and LODs by conventional PCR for GFB, GFC, and GFD

AssayTarget bacterial groupPrimer sequenceeMgCl2 concna (mM)Annealing temp (°C)Product size (bp)LOD
Plasmidb (no. of copies/reaction)Gull fecesc (mg feces/100 ml)Enterococci (MPN/100 ml)d
GFBUnclassified Fusobacterium spp.F 5′-TCA TGA AAG CTA TAT GCG CCA AAA1.5641762,000130
R 5′-TCC ATT GTC CAA TAT TCC CCA C
GFCCatellicoccus marimammaliumF 5′-CCC TTG TCG TTA GTT GCC ATC ATT C2.06916220130
R 5′-GCC CTC GCG AGT TCG CTG C
GFDUnclassified Helicobacter spp.F 5′-TCG GCT GAG CAC TCT AGG G1.0571232010194
R 5′-GCG TCT CTT TGT ACA TCC CA
  • a Final MgCl2 concentration in the reaction mixture.

  • b Defined as the lowest number of plasmids at which all PCR replicates amplified.

  • c Defined as the lowest fecal dilution at which all PCR replicates amplified.

  • d FIB in the lowest fecal dilution at which all PCR replicates amplified.

  • e F, forward; R reverse.