Inflammation of the small intestine
The epithelium of the small intestine is constantly exposed to a range of microorganisms and foreign substances. It provides both a physical and immunological barrier against these exterior challenges. The cells of the epithelium are constantly scanning the environment for antigens to be able to quickly react to pathogens. Antigens are foreign molecules that are recognized by the immune system.
If an antigen is detected by a lymphocyte, the immune cell sends out immunostimulators and a signaling cascade is initialized. More lymphocytes are recruited and they migrate into the inflamed tissue. Radical changes of the epithelial architecture lead to a decreased length of the villi, apoptosis of epithelial cells, and enlarged crypts. These changes decrease the surface area of the small intestine, which in turn leads to a decrease in the absorption of nutrients.
High numbers of lymphocytes in the epithelium are a clear sign of inflammation 
Coeliac disease
Gluten is a protein found in grains, such as wheat, barley, and rye. Gluten crosslinks starch fibers and gives dough its elasticity and chewiness. In genetically predisposed individuals, gluten is recognized as an antigen and triggers an immune response. Lymphocytes migrate into the epithelium of the small intestine and initiate an inflammatory reaction. If the person continues to consume gluten, the intestine remains chronically inflamed. This leads to the previously described shrinking of the villi and a decrease in the surface area of the small intestine. This severe form of gluten intolerance is called coeliac disease.
Patients suffer from chronic constipation, diarrhoea, anaemia, fatigue, and children fail to thrive. The damage induced to the intestinal lining remains for a long time and the only effective treatment is a gluten-free diet. Gluten intolerance remains undiagnosed in most patients, therefore it is unknown how many people are affected by it. Recent studies estimate around 1 % of the population of Western countries suffers from coeliac disease. 
Malabsorption syndrome in chicken
Malabsorption syndrome, also known as runting-stunting disease, occurs in young chickens and leads to a delay in growth of the affected individuals and an overall reduced productivity of the chicken farm. The disease is associated with several different virus strains, but a single agent has not been identified.
Healthy chickens can be infected with an inoculum of the intestinal content of a diseased individual.
The infected chickens develop enteric lesions, dilation of the crypts, and atrophy of the villi. These changes lead to a reduction in the absorptive surface area, which in turn leads to decreased nutrient uptake and reduced growth.