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Microbial source tracking (MST) identifies fecal sources of water contamination by detecting microbes found in the feces of humans, cattle, pigs, poultry, or other animals.

The Laboratory for Infectious Disease and the Environment (LIDE) analyzes MST microbes for humans, livestock, and wildlife. Results inform efforts to understand and address contamination. The LIDE can help guide selection of the MST tests relevant to your project goals, and they offer support for study design, sample collection, data analysis, and interpretation of MST results.

  • By identifying specific fecal sources, MST provides more information about water quality than general microbial indicators that can originate in many sources.
  • Results can be used with pathogen analyses to characterize the health risks posed by contamination, like from drinking tap water or swallowing water while swimming.  For example, we related human and livestock contamination of private wells to health risk in a rural, agricultural region.
  • Land use, rainfall, geology, and other factors related to fecal contamination can be investigated to support management efforts that protect water quality.  For example, we identified factors related to fecal contamination of private wells.


Microbial source tracking assays available for analysis by quantitative polymerase chain reaction (qPCR) at LIDE (additional qPCR assays are evaluated and optimized as needed):

Human Viruses and Bacteria Bovine Bacteria and Viruses

Human adenovirus groups A-F

Bovine adenovirus

Human enterovirus

Bovine enterovirus

Hepatitis A virus

Bovine polyomavirus

Human polyomavirus

Bovine viral diarrhea virus type 1

Norovirus genogroup I

Bovine viral diarrhea virus type 2

Bacteroidales-like HumM2

Bovine coronavirus

Clostridium perfringens

Bacteroidales-like cow M2

Human Bacteroides (HF183/BacR287)

Bacteroidales-like cow M3


Ruminant Bacteroides

Porcine Bacteria & Viruses



Other Bacteria and Viruses


Avian associated Bacteroidales

Porcine adenovirus

Poultry parvovirus

Porcine epidemic diarrhea virus

Gull Bacteroidales


Goose Bacteroidales

  Canine Bacteroides