Fecal waste form livestock such as cattle, swine and pultry raised in confined facilities is excreted onto the floors of the animal stalls or pens. Accumulation of this fecal material acts as a collection basin for pathogens that may spread between animals. Disposal of this domestic livestock fecal material may comprise of storage in lagoons or waste piles with the ultimate application to the incorporation into the soil. In the rearing of dmoestic livestock on range or pasture, manure may not be as concentrated in one area as with indoor livestock. These animals can also contaminate water by defication in unprotected surface water, through surface runoff and as a result of seepage of water through the soil that contains an excessive amount of manure.

To assess the threat posed by different micro-organisms in manure, pathogen survival in manure as it is usually handled on farms must be evaluated. Survivival of parasitic and bacterial pathogens is dependant on manure source, temperature, pH, dry matter content, age, chemical compostion of the manure as well as the microbial characteristics. Holding of manure as slurry, or as a solid compost before it is distributed, results ina significant redution in pathogen concentration.