Candida albicans is a fungus present in the normal flora of humans. An overgrowth of this fungus may cause yeast infections of the skin, vagina, or mouth. After a child receives antibiotics, they may contract a mycotic diaper rash due to Candida albicans overgrowth since the normal bacterial flora have been eliminated by the antibiotics. Pneumocystis jirovecii may cause pneumocystis pneumonia. Blastomyces dermatitidis and Aspergillus fumigatus may cause lung infection if the spores are inhaled. Lastly, Sporothrix schenckii may cause a skin infection called Sporotrichosis after it enters through a break in skin integrity.

Prions are infectious protein particles that affect proteins, misfolding them and causing loss of function. They are most commonly found in the brain. Prion diseases are also called transmissible spongiform encephalopathies (TSEs) and include diseases such as mad cow disease and Creutzfeldt-Jakob disease.

Fungi are similar to plants in that they both have cell walls (fungi have chitin cell walls and plants have cellulose cell walls) but they do not contain chlorophyll. Fungi such as Candida albicans are present in the normal flora of the human body. An overgrowth of fungi can cause mycotic infections such as a vaginal yeast infection, or orally as in thrush.

A retrovirus is an infectious particle consisting of an RNA genome packaged in a protein capsid, surrounded by a lipid envelope. This lipid envelope contains polypeptide chains, including receptor-binding proteins that link to the membrane receptors of the host cell, initiating the process of infection. In order to replicate, its genetic material (RNA) must first be converted to a DNA molecule by the enzyme reverse transcriptase. This enzyme, which is found in the virus particle, is a DNA polymerase that uses an RNA molecule as a template to synthesize DNA, resulting in an RNA/DNA double helix.

Further enzyme action leads to the synthesis of a DNA double helix using the RNA/DNA template. This DNA helix can then integrate into the host chromosome and be transcribed into RNA molecules coding for capsid proteins, envelope proteins, and the reverse transcriptase. This integration into the host DNA is carried out by the viral integrase. Integration into the host chromosome is required for the synthesis of new viral RNA molecules. A host cell RNA polymerase is responsible for this transcription. Many new virus particles are then assembled containing the RNA molecule and the enzyme reverse transcriptase.

Mononuclear phagocytes (MNPs), which consist of blood monocytes, tissue macrophages, and dendritic cells, are the main cellular elements responsible for elimination of viral pathogens. At the same time, MNPs are the targets and reservoirs for many viruses. Most noteworthy, the MNPs utilize phagocytosis as the first battle armament against the onslaught. This greatly diminishes the quantity of virus until other aspects of the immune system can be activated.

Utilizing a number of antimicrobial mechanisms, macrophages can prevent infection or replication of the virus in other cells, representing an additional protection mechanism. Antibodies produced in response to viral infection may lead to either neutralization or lysis of the target cells. This is partially governed by the macrophage, functioning nonspecifically as an effector cell for antibody dependent cellular cytotoxicity. In addition, both macrophages and monocytes can either activate or be activated upon by cytokines to further increase their antiviral vigilance.

The uptake, processing, and delivery of viral antigens to T cells in the lymph nodes referred to as antigen presentation rounds out the defense mechanisms utilized by macrophages. Monocytes and dendritic cells also function as antigen presenting cells.

Ghrelin is a hormone produced primarily in the stomach and small intestine. It is secreted when the stomach is empty, triggering a feeling of hunger. When the stomach is stretched, secretion of ghrelin is inhibited. Leptin is a hormone secreted by adipose cells to signal satiety. Gastrin triggers the secretion of stomach acid during digestion, and cholecystokinin (CKK) is a hormone with various roles in the process of digestion, primarily acting as a hunger suppressant and a trigger for the release of digestive enzymes and bile.

The ileocecal sphincter/valve separates the small intestine from the large intestine. The lower esophageal sphincter, also known as the cardiac sphincter, separates the esophagus from the stomach, while the pyloric sphincter separates the stomach from the small intestine.

The system of coordinated peristaltic waves that slowly sweeps food through the small intestine for digestion is called the migrating motor complex. Disorderly motion of this complex can result in a wide variety of gastrointestinal complaints such as vomiting, dumping syndrome, bloating, or indigestion. Segmentation contractions mix the contents of the colon for more absorption, while mass movements serve to propel feces towards the rectum. 

By the time the contents of the digestive tract ender the colon, the majority of food digestion is complete. The colon then serves primarily to absorb water and electrolytes and to prepare feces for excretion.

The duodenum wraps around the pancreas.