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Different causes

Food intolerance can have a number of different causes:

Enzyme defects

Enzymes are required to help with the breakdown of natural substances found in certain foods. If these enzymes are missing or in short supply, then eating the food can cause symptoms because the body cannot properly deal with part of the content of the food. 
We should remember that many foods contain chemicals that would be harmful if we could not detoxify them - the only reason we can eat, say, potatoes, but not deadly nightshade (which is part of the potato 'family') is because we have the enzymes to break down the toxins in one but not the other (cooking, of course, also helps). In lactose intolerance, for example, the body lacks the enzyme (lactase) that breaks lactose (milk-sugar) down into smaller sugars ready for absorption from the gut. Lactose is too large to be absorbed across the gut wall undigested, and its presence in the gut causes gut spasm, pain, bloating, diarrhoea and 'failure to thrive'. Incidentally, these same symptoms can occur in milk allergy, when the body has made antibodies to milk protein, which causes an immune reaction when you drink milk. Hence, you cannot always distinguish allergy from intolerance by symptoms alone. 
Most foods require some enzyme activity in their digestion, and enzyme deficiencies can be an important factor in food intolerance.

Pharmacological

Some foods contain naturally occurring ingredients that have an effect on the body, such as caffeine in coffee, tea and chocolate, or amines in certain cheeses. Some people seem to get a greater effect from these natural substances in the food, causing symptoms, which would not occur in other people unless they ate far larger quantities of the food. Often patients suffering this form of intolerance also have a history of greater side effects from medications.

Toxic

A number of foods contain naturally occurring substances that can exert a toxic effect in susceptible people. For example, some beans contain compounds called lectins that in some people can cause immune system cells to release the same chemicals that are released during an allergic reaction. This means that the person gets 'food allergy' symptoms when they eat the food, but they have not actually produced antibodies against the food and they are not, in fact, allergic to it.

Histamine in foods

Some foods contain histamine naturally, and others (such as certain fish that are not fresh and have not been stored properly) can develop a build-up of histamine in their flesh as they age. In certain people, this histamine occurring naturally in the food can cause symptoms when the food is eaten; typically, rashes, stomach pains, diarrhoea and vomiting.

Salicylates in foods

Many foods naturally contain salicylates, and our tolerance to this can vary. The vast majority of people can eat salicylate-containing foods with no problems, but other people may suffer symptoms if they eat too many foods, which in combination contain a large amount. These salicylate-intolerant people will get better if they eat a diet of low and moderate salicylate foods and avoid those with the highest levels.

Additives in foods

A wide variety of natural and artificial additives are used in colouring, preserving and processing foods. Some people can suffer symptoms provoked by hypersensitivity to food additives.

IgG antibodies to foods

Some people may make abnormal antibodies (IgG, different from the IgE that causes allergy), which mistakenly 'fight off' the food when they eat it. There is some evidence that food-related IgG may be involved in the development of symptoms such as irritable bowel syndrome, arthritis and migraine. However, IgG to foods is also found in the blood of people who do not suffer symptoms (and some people who do suffer do not have IgG). Food intolerance tends to develop to the foods that we eat most often (such as dairy products and grains); these are also the foods that most often have the highest levels of IgG.
Some people think that IgG in the blood for specific foods just relates to the foods that we eat most often, rather than necessarily meaning that they are doing us any harm. Research is ongoing to try to understand the relevance of IgG reactions in food intolerance.

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