Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces

Water Res. 2009 Nov;43(19):4860-71. doi: 10.1016/j.watres.2009.08.017. Epub 2009 Aug 22.


We measured the concentrations of four host-specific (human, dog, cow, and horse Bacteroidales), four generic fecal (16S total Bacteroidales and Escherichia coli, 23S Enterococcus and uidA E. coli,) and two universal bacterial (16S universal and rpoB universal) DNA targets by qPCR in raw sewage and pooled fecal samples from dogs, cows, horses, and Canada Geese. A spiking protocol using the non-fecal bacterium Pseudomonas syringae pph 6 was developed to estimate the recovery of DNA from fecal and environmental samples. The measured fecal marker concentrations were used to calculate baseline ratios and variability of host-specific to generic indicators for each host type. The host-specific markers were found in high concentrations (8-9 log(10)copies/g dry wt.) in their respective hosts' samples, which were equal to or greater than the concentrations of generic E. coli and Enterococcus markers, lending support to the use of host-specific and generic Bacteroidales as sensitive indicators of fecal pollution. The host-specific markers formed a consistent percentage of total Bacteroidales in target host feces and raw sewage, with human-specific comprising 82%, dog-specific 6%, cow-specific 4% and horse-specific 2%. Based on this limited data set, the measurement of host-specific indicators by qPCR has several promising applications. These applications include determining the percentage of total Bacteroidales contributed by a specific host type, using the ratios of host-specific markers to E. coli or Enterococcus to estimate the contribution of each source to these regulated fecal indicator bacteria, and estimating the mass of feces from each host type in environmental samples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacteroidetes / genetics
  • Bacteroidetes / isolation & purification
  • Cattle
  • DNA, Bacterial / genetics
  • Dogs
  • Enterococcus / genetics
  • Enterococcus / isolation & purification
  • Environmental Monitoring / methods*
  • Escherichia coli / genetics
  • Escherichia coli / isolation & purification
  • Feces / microbiology*
  • Humans
  • Polymerase Chain Reaction
  • Pseudomonas / genetics
  • Pseudomonas / isolation & purification
  • RNA, Ribosomal, 16S / genetics
  • Sewage / microbiology*
  • Species Specificity


  • DNA, Bacterial
  • RNA, Ribosomal, 16S
  • Sewage