See also The Decomposition of Human Remains
Decomposition begins at the moment of death, caused by two factors: 1.) autolysis, the breaking down of tissues by the body's own internal chemicals and enzymes, and 2.) putrefaction, the breakdown of tissues by bacteria. These processes release compounds such as cadaverine and putrescine, that are the chief source of the unmistakably putrid odor of decaying animal tissue.
Prime decomposers are bacteria or fungi, though larger scavengers also play an important role in decomposition if the body is accessible to insects, mites and other animals. The most important arthropods that are involved in the process include carrion beetles, mites, the flesh-flies (Sarcophagidae) and blow-flies (Calliphoridae), such as the green-bottle fly seen in the summer. In North America, the most important non-insect animals that are typically involved in the process include mammal and bird scavengers, such as coyotes, dogs, wolves, foxes, rats, crows and vultures. Some of these scavengers also remove and scatter bones, which they ingest at a later time. Aquatic and marine environments have break-down agents that include bacteria, fish, crustaceans, fly larvae  and other carrion scavengers.
Stages of decomposition
Five general stages are used to describe the process of decomposition in vertebrate animals: fresh, bloat, active decay, advanced decay, and dry/remains. The general stages of decomposition are coupled with two stages of chemical decomposition: autolysis and putrefaction. These two stages contribute to the chemical process of decomposition, which breaks down the main components of the body. With death the microbiome of the living organism collapses and is followed by the necrobiome that undergoes predictable changes over time.
Among those animals that have the heart, the "fresh" stage begins immediately after the heart stops beating. From the moment of death, the body begins cooling or warming to match the temperature of the ambient environment, during a stage called algor mortis. Shortly after death, within three to six hours, the muscular tissues become rigid and incapable of relaxing, during a stage called rigor mortis. Since blood is no longer being pumped through the body, gravity causes it to drain to the dependent portions of the body, creating an overall bluish-purple discolouration termed livor mortis or, more commonly, lividity.
Once the heart stops, the blood can no longer supply oxygen or remove carbon dioxide from the tissues. The resulting decrease in pH and other chemical changes causes cells to lose their structural integrity, bringing about the release of cellular enzymes capable of initiating the breakdown of surrounding cells and tissues. This process is known as autolysis.
Visible changes caused by decomposition are limited during the fresh stage, although autolysis may cause blisters to appear at the surface of the skin.
The small amount of oxygen remaining in the body is quickly depleted by cellular metabolism and aerobic microbes naturally present in respiratory and gastrointestinal tracts, creating an ideal environment for the proliferation of anaerobic organisms. These multiply, consuming the body's carbohydrates, lipids, and proteins, to produce a variety of substances including propionic acid, lactic acid, methane, hydrogen sulfide, and ammonia. The process of microbial proliferation within a body is referred to as putrefaction and leads to the second stage of decomposition, known as bloat.
Blowflies and flesh flies are the first carrion insects to arrive, and they seek a suitable oviposition site.
The bloat stage provides the first clear visual sign that microbial proliferation is underway. In this stage, anaerobic metabolism takes place, leading to the accumulation of gases, such as hydrogen sulfide, carbon dioxide, methane, and nitrogen. The accumulation of gases within the bodily cavity causes the distention of the abdomen and gives a cadaver its overall bloated appearance. The gases produced also cause natural liquids and liquefying tissues to become frothy. As the pressure of the gases within the body increases, fluids are forced to escape from natural orifices, such as the nose, mouth, and anus, and enter the surrounding environment. The buildup of pressure combined with the loss of integrity of the skin may also cause the body to rupture.
Intestinal anaerobic bacteria transform haemoglobin into sulfhemoglobin and other colored pigments. The associated gases which accumulate within the body at this time aid in the transport of sulfhemoglobin throughout the body via the circulatory and lymphatic systems, giving the body an overall marbled appearance.
If insects have access, maggots hatch and begin to feed on the body's tissues. Maggot activity, typically confined to natural orifices, and masses under the skin, causes the skin to slip, and hair to detach from the skin. Maggot feeding, and the accumulation of gases within the body, eventually leads to post-mortem skin ruptures which will then further allow purging of gases and fluids into the surrounding environment. Ruptures in the skin allow oxygen to re-enter the body and provide more surface area for the development of fly larvae and the activity of aerobic microorganisms. The purging of gases and fluids results in the strong distinctive odors associated with decay.
Active decay is characterized by the period of greatest mass loss. This loss occurs as a result of both the voracious feeding of maggots and the purging of decomposition fluids into the surrounding environment. The purged fluids accumulate around the body and create a cadaver decomposition island (CDI). Liquefaction of tissues and disintegration become apparent during this time and strong odors persist. The end of active decay is signaled by the migration of maggots away from the body to pupate.
Decomposition is largely inhibited during advanced decay due to the loss of readily available cadaveric material. Insect activity is also reduced during this stage. When the carcass is located on soil, the area surrounding it will show evidence of vegetation death. The CDI surrounding the carcass will display an increase in soil carbon and nutrients, such as phosphorus, potassium, calcium, and magnesium; changes in pH; and a significant increase in soil nitrogen.
During the dry/remains stage, the resurgence of plant growth around the CDI may occur and is a sign that the nutrients present in the surrounding soil have not yet returned to their normal levels. All that remains of the cadaver at this stage is dry skin, cartilage, and bones, which will become dry and bleached if exposed to the elements. If all soft tissue is removed from the cadaver, it is referred to as completely skeletonized, but if only portions of the bones are exposed, it is referred to as partially skeletonised.
Pig carcass in the different stages of decomposition: Fresh > Bloat > Active decay > Advanced decay > Dry remains