Microbial source tracking (MST) is a term used for the process of identifying the source of fecal contamination in the environment.
Identifying and mitigating the source of fecal contamination to a particular waterbody is complicated by the fact that traditional measures of fecal bacteria concentrations are not host-specific.
Microbial source tracking (MST) techniques are based on the concept that various warm-blooded animal intestinal systems have different selective pressures caused by differences such as diet and physiology that select for specific gut microbial populations. MST attempts to utilize the unique microbial populations by host animal through identifying some unique genetic (DNA or RNA sequence) or phenotypic (observable characteristic or expression, such as antibiotic resistance) trait.
Although no standard methods exist for MST, host-associated genetic markers, also known as MST markers, have been developed to detect and quantify fecal contamination from sources including human, canine, ruminant, cattle, horse, swine, chicken, and waterfowl.