Decomposition is the process by which organic substances are broken down into simpler matter. The process is a part of nutrient cycle and is essential for recycling the finite matter that occupies physical space in the biosphere. Bodies of living organisms begin to decompose shortly after death. Animals, such as worms, also help decompose the organic materials. Organisms that do this are known as decomposers. Although no two organisms decompose in the same way, they all undergo the same sequential stages of decomposition. The science which studies decomposition is generally referred to as "taphonomy" from the Greek word "taphos", meaning tomb.

One can differentiate abiotic from biotic decomposition (biodegradation). The former means "degradation of a substance by chemical or physical processes, e.g., hydrolysis. The latter means "the metabolic breakdown of materials into simpler components by living organisms", typically by microorganisms.

Biodegradation is the disintegration of materials by bacteria, fungi, or other biological means.

The term is often used in relation to: biomedicine, waste management, ecology, and the bioremediation of the natural environment. It is now commonly associated with environmentally-friendly products, capable of decomposing back into natural elements.

Although often conflated, "biodegradable" is distinct in meaning from: "compostable". While biodegradable simply means "can be consumed by microorganisms", "compostable" makes the further specific demand that the object break down under composting conditions.

Organic material can be degraded aerobically (with oxygen) or anaerobically (without oxygen). Decomposition of biodegradable substances may include both biological and abiotic steps.

Biodegradable matter is generally organic material that provides a nutrient for microorganisms. These are so numerous and diverse that a huge range of compounds can be biodegraded, including hydrocarbons (oils), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and pharmaceutical substances.

Microorganisms secrete biosurfactant, an extracellular surfactant, to enhance this process.

Citrus Black Spot is a fungal disease caused by Guignardia citricarpa. This Ascomycete fungus affects citrus plants throughout subtropical climates, causing a reduction in both fruit quantity and quality. Symptoms include both fruit and leaf lesions, the latter being critical to inter-tree dispersal. Strict regulation and management is necessary to control this disease since there are currently no citrus varieties that are resistant.

The disease is characterised by the formation of painful abscesses in the mouth, lungs, breast, or gastrointestinal tract. Actinomycosis abscesses grow larger as the disease progresses, often over months. In severe cases, they may penetrate the surrounding bone and muscle to the skin, where they break open and leak large amounts of pus, which often contains characteristic granules (sulfur granules) filled with progeny bacteria. These granules are named due to their appearance, but are not actually composed of sulfur.

Anaerobes can be isolated from most types of upper respiratory tract and head and neck and infection and are especially common in chronic ones. These include tonsillar, peritonsillar and retropharyngeal abscesses, chronic otitis media, sinusitis and mastoiditis, eye ocular) infections, all deep neck space infections, parotitis, sialadenitis, thyroiditis, odontogenic infections, and postsurgical and nonsurgical head and neck wounds and abscesses., The predominant organisms are of oropharyngeal flora origin and include AGNB, "Fusobacterium" and Peptostreptococcus spp.

Anaerobes involve almost all dental infections. These include dental abscesses, endodontal pulpitis and periodontal (gingivitis and periodontitis) infections, and perimandibular space infection. Pulpitis can lead to abscess formation and eventually spread to the mandible and other neck spaces. In addition to strict anaerobic bacteria, microaerophilic streptococci and "Streptococcus salivarius" can also be present.

"Fusobacterium" spp. and anaerobic spirochetes are often the cause of acute necrotizing ulcerative gingivitis (or Vincent's angina) which is a distinct form of ulcerative gingivitis.

Deep neck infections that develop as a consequence of oral, dental and pharyngeal infections are generally polymicrobial in nature. These include extension of retropharyngeal cellulitis or abscess, mediastinitis following esophagus perforation, and dental or periodontal abscess.

Dental plaque is a biofilm or mass of bacteria that grows on surfaces within the mouth. It is a sticky colorless deposit at first, but when it forms tartar, it is often brown or pale yellow. It is commonly found between the teeth, on the front of teeth, behind teeth, on chewing surfaces, along the gumline, or below the gumline cervical margins. Dental plaque is also known as microbial plaque, oral biofilm, dental biofilm, dental plaque biofilm or bacterial plaque biofilm.

Progression and build-up of dental plaque can give rise to tooth decay – the localised destruction of the tissues of the tooth by acid produced from the bacterial degradation of fermentable sugar – and periodontal problems such as gingivitis and periodontitis; hence it is important to disrupt the mass of bacteria and remove it. Plaque control and removal can be achieved with correct daily or twice-daily tooth brushing and use of interdental aids such as dental floss and interdental brushes.

Oral hygiene is important as dental biofilms may become acidic causing demineralization of the teeth (also known as dental caries) or harden into dental calculus (also known as tartar). Calculus cannot be removed through tooth brushing or with interdental aids, but only through professional cleaning.

"Actinomycosis" is a rare infectious bacterial disease caused by "Actinomyces" species. About 70% of infections are due to either "Actinomyces israelii" or "A. gerencseriae". Infection can also be caused by other "Actinomyces" species, as well as "Propionibacterium propionicus", which presents similar symptoms. The condition is likely to be polymicrobial aerobic anaerobic infection.

False melanose lesions are characterized by many small, tan, slightly raised lesions. The lesions are much smaller than the hard spot variety with an average diameter of less than 1 mm (.04 in).

They are found on unripe fruit and are difficult to observe later in the season. Unlike hard spot lesions, no pycnidia are present.

Secondary peritonitis and intra-abdominal abscesses including splenic and hepatic abscesses generally occur because of the entry of enteric micro-organisms into the peritoneal cavity through a defect in the wall of the intestine or other viscus as a result of obstruction, infarction or direct trauma. Perforated appendicitis, diverticulitis, inflammatory bowel disease with perforation and gastrointestinal surgery are often associated with polymicrobial infections caused by aerobic and anaerobic bacteria, where the number of isolates can average 12 (two-thirds are generally anaerobes). The most common aerobic and facultative bacteria are "Escherichia coli", "Streptococcus" spp. (including Enterococcus spp.), and the most frequently isolated anaerobic bacteria are the "B. fragilis" group, "Peptostreptococcus" spp., and "Clostridium" spp.

Abdominal infections are characteristically biphasic: an initial stages of generalized peritonitis associated with "Escherichia coli" sepsis, and a later stages, in which intra abdominal abscesses harboring anaerobic bacteria ( including "B. fragilis" group ) emerge.

The clinical manifestations of secondary peritonitis are a reflection of the underlying disease process. Fever, diffuse abdominal pain, nausea and vomiting are common. Physical examination generally show signs of peritoneal inflammation, isuch as rebound tenderness, abdominal wall rigidity and decrease in bowel sounds. These early findings may be followed by signs and symptoms of shock.

Biliary tract infection is usually caused by "E. coli, Klebsiella" and "Enterococcus" spp. Anaerobes (mostly "B. fragilis" group, and rarely "C. perfringens") can be recovered in complicated infections associated with carcinoma, recurrent infection, obstruction, bile tract surgery or manipulation.

Laboratory studies show elevated blood leukocyte count and predominance of polymorphonuclear forms. Radiographs studies may show free air in the peritoneal cavity, evidence of ileus or obstruction and obliteration of the psoas shadow. Diagnostic ultrasound, gallium and CT scanning may detect appendiceal or other intra-abdominal abscesses. Polymicrobial postoperative wound infections can occur.

Treatment of mixed aerobic and anaerobic abdominal infections requires the utilization of antimicrobials effective against both components of the infection as well as surgical correction and drainage of pus. Single and easily accessible abscesses can be drained percutaneously.

In dentistry, calculus or tartar is a form of hardened dental plaque. It is caused by precipitation of minerals from saliva and gingival crevicular fluid (GCF) in plaque on the teeth. This process of precipitation kills the bacterial cells within dental plaque, but the rough and hardened surface that is formed provides an ideal surface for further plaque formation. This leads to calculus buildup, which compromises the health of the gingiva (gums). Calculus can form both along the gumline, where it is referred to as supragingival ("above the gum"), and within the narrow sulcus that exists between the teeth and the gingiva, where it is referred to as subgingival ("below the gum").

Calculus formation is associated with a number of clinical manifestations, including bad breath, receding gums and chronically inflamed gingiva. Brushing and flossing can remove plaque from which calculus forms; however, once formed, it is too hard and firmly attached to be removed with a toothbrush. Calculus buildup can be removed with ultrasonic tools or dental hand instruments (such as a periodontal scaler).

Interdigital dermatitis appears as an infections of the skin between the claws and is usually very mild. There may be fluid or a scab in that area, and there is rarely lameness. There is then progression to the heels which become raw and cattle will experience pain. Chronic cases will show changes of the hoof including hyperplasia of the interdigital tissues and muscle atrophy in the affected limb. The horn may become underrun.

Diagnosis is principally based on history and clinical signs. It is very rare that attempts are made to isolate the bacteria.

Putrefaction is the fifth stage of death, following pallor mortis, algor mortis, rigor mortis, and livor mortis. This process references the breaking down of a body of a human or animal post mortem (meaning after death). In broad terms, it can be viewed as the decomposition of proteins, and the eventual breakdown of the cohesiveness between tissues, and the liquefaction of most organs. This is caused by the decomposition of organic matter by bacterial or fungal digestion, which causes the release of gases that infiltrate the body's tissues, and leads to the deterioration of the tissues and organs.

The approximate time it takes putrefaction to occur is dependent on various factors. Internal factors that affect the rate of putrefaction include the age at which death has occurred, the overall structure and condition of the body, the cause of death, and external injuries arising before or after death. External factors include environmental temperature, moisture and air exposure, clothing, burial factors, and light exposure.

The first signs of putrefaction are signified by a greenish discoloration on the outside the skin on the abdominal wall corresponding to where the large intestine begins, as well as under the surface of the liver.

Certain substances, such as carbolic acid, arsenic, strychnine, and zinc chloride, can be used to delay the process of putrefaction in various ways based on their chemical make up. At body farms, facilities which study the process of decomposition as well as how these substances affect the rate of putrefaction, cadavers are put in different environmental conditions to study how the process of decomposition can be affected. There are six University Body Farm Research Facilities in the world, all located within the United States, which include the University of Tennessee at Knoxville, Western Carolina University, Texas State University, Sam Houston State University, Southern Illinois University, and Colorado Mesa University. Two prospective body farms will open outside the United States, in Australia and India.

Interdigital dermatitis in cattle is caused by the anaerobic bacterium "Dichelobacter nodosus". This is also the agent of footrot in sheep, but strains appear to be different and there is no cross-infection.

Interdigital dermatitis is different from footrot in cattle and both conditions may occur concurrently.

The condition most commonly occurs in farms with a high stocking density or where cattle traffic is high and is most prevalent in Winter.

The first sign of a foot-rot infection is when the skin between the claws of the hoof begins to swell (cellulitis). Swelling usually appears 24 hours after infection. The skin between the toes may be very red and tender and the toes may separate because of all the swelling. This is very painful to the animal and can cause lameness. The animal may also have a raised body temperature. A crack can develop along the infected part and is yellow in color. The foot will have a foul odor. Tendons and joints in the area can become infected, which is much harder to treat. A condition known as "super foot rot" is seen in some animals. Super foot rot infection occurs much faster and is usually much more severe. Most normal foot rot treatments will not cure this foot rot and a veterinarian should be contacted immediately.

Vaccines have been developed, but their efficacy is questionable and the immunity they provide is of short duration.

Foot rot, or infectious pododermatitis, is a hoof infection commonly found in sheep, goats, and cattle. As the name suggests, it rots away the foot of the animal, more specifically the area between the two toes of the affected animal. It is extremely painful and contagious. It can be treated with a series of medications, but if not treated, the whole herd can become infected. The cause of the infection in cattle is two species of anaerobic bacteria, "Fusobacterium necrophorum" and "Bacteroides melaninogenicus". Both bacteria are common to the environment in which cattle live, and "Fusobacterium" is present in the rumen and fecal matter of the cattle. In sheep, "F. necrophorum" first invades the interdigital skin following damage to the skin, and causes interdigital lesions and slight inflammation. The second stage of the disease is marked by the invasion of the foot by the foot rot bacterium "Dichelobacter nodosus", a Gram-negative anaerobe. Usually, an injury to the skin between the hooves allows the bacteria to infect the animal. Another cause of foot rot may be high temperatures or humidity, causing the skin between the hooves to crack and let the bacteria infect the foot. This is one of the reasons foot rot is such a major problem in the summer. Foot rot is easily identifiable by its appearance and foul odor. Treatment is usually with an antibiotic medication, and preventing injury to the feet is the best way to prevent foot rot.

The disease is different in cattle and sheep and cross-infection is not thought to occur.

Digital dermatitis appears as lesions which initially looks like raw, red, oval ulcer on the back of the heel. These lesions develop raised, hair-like projections or wart-like lesions, and some may extend up between the claws or appear on the front of the foot.

A scoring system was developed to classify the different stages of digital dermatitis, the M-stages system, where "M" stands for Mortellaro. The different stages are described as: M0, healthy skin; M1, early stage, skin defect < 2 cm diameter; M2, acute active ulcerative lesion; M3, healing stage, lesion covered with scab-like material; M4, chronic stage, that may be dyskeratotic (mostly thickened epithelium) or proliferative or both.

Diagnosis is principally based on history and clinical signs. It is very rare that attempts are made to isolate the bacteria.

Age of Death: Stillborn fetuses and infants putrefy slowly due to their sterility. Generally, younger people putrefy more quickly than older people.

Condition of the Body: A body with a greater fat percentage and less lean body mass will have a faster rate of putrefaction, as fat retains more heat and it carries a larger amount of fluid in the tissues.

Cause of Death: The cause of death has a direct relationship to putrefaction speed, with bodies that died from acute violence or accident generally putrefying slower than those that died from infectious diseases. Certain poisons, such as potassium cyanide or strychnine may also delay putrefaction, while chronic alcoholism will speed it.

External Injuries: Antemortem or postmortem injuries can speed putrefaction as injured areas can be more susceptible to invasion by bacteria.

Digital dermatitis is a disease that causes lameness in cattle. It was first discovered in Italy in 1974 by Cheli and Mortellaro. This disease is caused by a mixture of different bacteria. Anaerobic bacteria, including spirochetes of the genus "Treponema", are found in the lesions associated with the infection. Digital dermatitis is different from foot rot in cattle and both conditions may occur concurrently.

Digital dermatitis primarily affects dairy cattle and has been known to lower the quantity of milk produced, but the quality of the milk is unaffected.

Evidence show that risk factors favouring digital dermatitis outbreaks include: poor hygiene and high humidity; introduction of infected animals; no hoof care for heifers and dry cows; high levels of chronically infected animals; insufficient or inadequate hoof trimming; soft hooves and unbalanced nutrition.

In the early stages, periodontitis has very few symptoms, and in many individuals the disease has progressed significantly before they seek treatment.

Symptoms may include:

- Redness or bleeding of gums while brushing teeth, using dental floss or biting into hard food (e.g., apples) (though this may occur even in gingivitis, where there is no attachment loss)

- Gum swelling that recurs

- Spitting out blood after brushing teeth

- Halitosis, or bad breath, and a persistent metallic taste in the mouth

- Gingival recession, resulting in apparent lengthening of teeth. (This may also be caused by heavy-handed brushing or with a stiff toothbrush.)

- Deep pockets between the teeth and the gums (pockets are sites where the attachment has been gradually destroyed by collagen-destroying enzymes, known as collagenases)

- Loose teeth, in the later stages (though this may occur for other reasons, as well)

Patients should realize gingival inflammation and bone destruction are largely painless. Hence, people may wrongly assume painless bleeding after teeth cleaning is insignificant, although this may be a symptom of progressing periodontitis in that patient.

The "severity" of disease refers to the amount of periodontal ligament fibers that have been lost, termed "clinical attachment loss". According to the American Academy of Periodontology, the classification of severity is as follows:

- Mild: of attachment loss

- Moderate: of attachment loss

- Severe: ≥ of attachment loss

Among those animals that have a 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 cause 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 word comes from Latin "calculus" "small stone", from "calx" "limestone, lime", probably related to Greek "chalix" "small stone, pebble, rubble" which many trace to a Proto-Indo-European root for "split, break up". "Calculus" was a term used for various kinds of stones. This spun off many modern words, including "calculate" (use stones for mathematical purposes), and "calculus", which came to be used, in the 18th century, for accidental or incidental mineral buildups in human and animal bodies, like kidney stones and minerals on teeth.

Tartar, on the other hand, originates in Greek as well ("tartaron"), but as the term for the white encrustation inside casks, aka potassium bitartrate commonly known as cream of tartar. This came to be a term used for calcium phosphate on teeth in the early 19th century.

When infection begins, the animal may develop a fever, and the affected limb can feel hot to the touch. The limb usually swells significantly, and the animal can develop lameness on the affected leg. Crepitation (the sensation of air under the skin) can be noticed in many infections, as the area seems to crackle under pressure.

Once clinical signs develop, the animal may only live a short while, sometimes as few as 12 hours. Occasionally, cattle succumb to the disease without showing any symptoms, and only a necropsy reveals the cause. During a necropsy, a diagnosis is usually made very quickly, as the affected muscle is usually mottled with black patches, which are dead tissue, killed by the toxins the bacteria release when they infect live tissue. If viewed under a microscope, small rod-like bacteria can be seen to confirm the diagnosis.

Symptoms

- Pain right hypochondrium referred to right shoulder

- Pyrexia (100.4 F)

- Profuse sweating and rigors

- Loss of weight

- Earthy complexion

Signs

- Pallor

- Tenderness and rigidity in right hypochondrium

- Palpable liver

- tenderness

- Basal lung signs

Blackleg, black quarter, quarter evil, or quarter ill () is an infectious bacterial disease most commonly caused by "Clostridium chauvoei", a Gram-positive bacterial species. It is seen in livestock all over the world, usually affecting cattle, sheep, and goats. It has been seen occasionally in farmed bison and deer. The acute nature of the disease makes successful treatment difficult, but an effective vaccine is available to provide animals with protective immunity.