Manure, if handled properly can be an asset for crop production.  If handled improperly, manure can become a liability and the subject of a lawsuit.  Many nuisance lawsuits list odors, dust, and flies together as components in the suit. 
Cattle manure in a pasture setting provides a habitat for 35-40 species of insects.  Horn flies and face flies are the most notable inhabitants of the pasture manure because of their pest status with animals.  But there are many other species that feed on the manure (recycle) or are predators and parasites of insects that use manure for development. 
   In a confined animal setting, manure is quickly adulterated with soil and moisture and becomes the developmental medium for another complex of insects; although some species of insects overlap and are present in either pasture or confined livestock manure.  The major pests of confined livestock manure are the house fly and the stable fly.  The house fly can complete it's life cycle from egg to adult in about two weeks during summer months.  The stable fly requires an additional week to complete it's life cycle.  Their life cycles are similar and are comprised of eggs, larvae (maggots), pupae, and adults.  Both species have high reproductive rates of 200-800 eggs per female.  This factor, combined with short life cycles, may result in very high fly population levels particularly during wet years. 
   The economics of the house fly in terms of livestock production is unclear.  House flies are known to be vectors of several diseases of man and animals but do not appear to directly affect animal production.  They are, however, important from the standpoint of lawsuits. 
  Stable flies feed on animal blood and, in so doing, inflict a painful bite as they inject their mouthparts into the skin.  Animals react to attack by stable flies by bunching with each animal attempting to protect it's front legs.  Losses in feedlot cattle weight gain of as much as 0.48 lbs/animal/day have been recorded.  Research indicates about 70% of the decrease in weight gain is the result of heat stress induced by the bunching behavior and 30% is due to blood loss and energy loss from fighting the flies. 
Common manure accumulation areas at confined livestock units that result in high fly populations have been identified.  Trapping flies in some of these areas have resulted in catches of more than 8,000 flies per square meter of manure, soil and moisture mixture such as found adjacent to feeding aprons.  Other major areas that are often major fly breeding sources include:  1) under fence lines, 2) next to feedbunks, 3) along leaky waterers, 4) drainage areas along pen mounds, 5) drainage areas away form the pens, 6) debris basins, 7) around feeding racks at dairies, 8) in and around calf hutches, 9) in and around loafing sheds, and 10) silage and haylage drainage areas.  Inside confined livestock units may have fly breeding occurring in the pits if the material is allowed to crust and in the corners of the pit if these areas aren't cleaned. 
  There may be considerable fly breeding at stored manure sites if the manure isn't stacked and packed in a manner which prevents water penetration.  Covering the manure with black plastic will prevent problems.  Manure spread on cropland may provide a fly-breeding area if the material isn't incorporated into the soil prior to rain. 
A successful fly control program requires good manure management, strict sanitation and, generally, some use of insecticides.  The most commonly used insecticides are space sprays applied through a mist blower.  The small insecticide droplets are circulated through the fly-infested area by the blower and flies are killed after contact by the insecticide droplet.  Some research indicates that the small wasp fly-pupal parasites available commercially may be effective.  We haven't experienced that success with our research.  However, neither the insecticides not the parasites have a chance of being successful unless good manure management and sanitation is practiced.