What is Microbial Source Tracking?

Microbial source tracking (MST) is a method used to identify the sources of fecal contamination in environmental samples, such as water, soil, and sediment. Using a suite of DNA based assays that target regions of the genome of certain gut-bacteria that are associated with a variety of host sources (animals or humans) the origins of fecal contamination can be identified.

Why is fecal contamination a concern?

Fecal contamination in the environment can pose a risk to public health by transmitting pathogens that cause illness. Water contaminated with pathogens can lead to severe outbreaks when it is used for example for water recreation, shellfish harvesting, as irrigation for crops or as drinking water. The primary benefit of MST studies is that with known sources the appropriate management strategies can be selected to reduce the contamination. MST is thus an important tool that helps watershed managers protect public health by targeting interventions to reduce the risk of pathogen transmission.

What are use cases for MST?

Microbial source tracking (MST) has a variety of use cases across different sectors. Here are some examples:

1. MST can be used to track down the sources of fecal contamination in waterways, such as rivers, lakes, and oceans. This information can be used to implement targeted management strategies to reduce fecal contamination and improve water quality. Besides protecting public health, avoiding beach closures also has economic benefits.
2. MST can be applied to assess the effectiveness of wastewater treatment plants by identifying the sources of fecal contamination in the treated wastewater. This can help determine if the treated wastewater is safe for discharge into the environment.
3. MST can also be used to identify the source of food-borne illness outbreaks by tracing the origins responsible for the outbreak and identifying pathways of fecal contamination.
4. Another use case of MST is to evaluate the impact of animal agriculture on water quality by identifying the sources of fecal contamination in waterways near livestock farms. Such information can help highlight areas where agricultural practices need to be improved to protect water quality.
5. MST can be employed to identify sources of fecal contamination in shellfish harvesting areas, implement management strategies and protect public health.
6. Further, MST can be implemented to monitor the effectiveness of best management practices (BMPs), such as the use of riparian buffers and cover crops, in reducing fecal contamination in waterways. This can help identify which practices are most effective and guide future management decisions.
7. Another use case for MST is the application in epidemiological investigations to identify the source of outbreaks of waterborne or food-borne illness caused by fecal pathogens.

How is MST testing different to other genomic identification methods?

In contrast to methods for the identification of certain animal species or pathogens, microbial source tracking assays don’t identify the source species (e.g. cow), but the gut bacteria that have adapted to the specific conditions (based on diet and animal specific properties) of their hosts. More precisely, MST assays target gene sequences in common gut bacteria (Bacteroidales, Helicobacter, Catellicoccus, Lachnospiraceae, etc.) that are specific for the host. Gut microbiome studies have shown that there is not a single bacteria species that occurs in every single individual host species. In other words, the commonly used HF83 marker that is used to identify human fecal sources is found in most individuals but not in every single person. This is of course in contrast to species specific assays for which a tissue sample of a certain fish species will always carry the species specific DNA.

What Microbial Source Tracking assays do we offer?

We carry a wide variety of different MST markers. All our assays are from peer-reviewed publications and have been validated thoroughly. The selection of specific assays can depend on study goals, regional preferences, regulator input or historic data. If the assay you are looking for is not in the list below, please inquire.