In order to treat this gut problem, the diet must be cleaned up first.  In our clinical work we recommend an organic diet, not one that is genetically modified or engineered.  The “right” diet can be:

GFCF
GFCF, soy and corn free
Specific Carbohydrate Diet (SCD)
GAPS diet
Low phenol
Low Salicylate
Low Oxalate
Reduced glutamate/aspartate diet
Ketogenic diet
Allergy/sensitivity elimination/rotation diet

One of the problems created by the vitamin deficiencies that occur within a leaky gut is vitamin B12 deficiency. B12 absorption is inhibited early in this process as microbes enter the small intestine because B12 is absorbed in the ileum, the last segment of the small intestine. Vitamin B12 is essential for the metabolism of fats and carbohydrates and the synthesis of proteins. Vitamin B12 is involved in the manufacture of the myelin sheath, the fatty layer that insulates the nerves in the brain. It is also essential for the formation of neurotransmitters and repair of damaged, flattened microvilli in the intestine. With sufficient B12 and folic acid in the bloodstream, the intestinal cells and microvilli can rejuvenate every 3 to 4 days. However, most children in the autistic spectrum have metabolic abnormalities in folate and B12 metabolism and cannot utilize these vitamins in the natural state. The latest studies have shown that 75% of patients on the autism spectrum and their mothers have cerebral folate antibodies which interfere with the metabolic pathways affecting neurotransmitter and glutathione production, among others. In the normal intestinal tract the small intestine and stomach are not inhabited by bacteria. When the bacterial balance in the colon is lost or when the gut is never colonized with ‘good’ bacteria, the microbes can migrate into the small intestine and stomach, hampering digestion. They compete for nutrients and their waste products overrun the intestinal tract. Yeast has the ability to produce toxins that actually allow them to bore into the intestinal wall. They also produce toxins such as organic acids which can damage the intestinal wall. Bacterial growth in the small intestine destroys enzymes on the intestinal cell surface, which prevents carbohydrate digestion and absorption. The final stage of carbohydrate digestion takes place at the microvilli. Enzymes embedded in the microvilli break down complex carbohydrates so they can be absorbed properly and enter the blood stream. When the microvilli are damaged, the last stage of digestion cannot take place. At this point only monosaccharides, or simple carbohydrates can be absorbed because of their single molecule structure. The complex carbohydrates can cause overgrowth of bacteria and yeast. In the small intestine, the body should absorb the nutrients needed from what is eaten. In the case of malabsorption, the undigested carbohydrates left in the small intestine cause the body to draw water into the intestinal tract. This pushes undigested carbohydrates into the colon where the microbes can feed on them. This allows further proliferation of the unwanted microbes and continued increase in malabsorption problems.autistic children have significantly lower intestinal carbohydrate digestive enzyme activity. 

Cleaning up the Diet

Avoiding genetically modified foods such as soy, corn, potatoes which can lead to unexpected allergic reactions and changes in the digestive tract.
Avoiding genetically engineered foods containing certain bacteria that is lethal to living cells.
Gluten – while celiac testing is often negative, it is known that gluten can set off distinct reaction in the intestines and the immune system even in people who don’t have celiac disease. Gluten sensitivity and gluten sensitive enteropathy have been associated with ataxia, migraine, dementia, seizures, visual and auditory disturbances, hypotonnia, depression, anxiety, fibromyalgia and chronic fatigue.
Bovine casomorphin, similar to opiates has been shown to affect the brain maturation, decrease cysteine, glutathione and methionine levels in neuronal cells.  Milk-free diet affects folate receptor autoimmunity in cerebral folate deficiency syndromes which occurs in 75% of autistic patients and their mothers.
Phenols affect sulphation which can lead to metabolic dysfunction (Waring, 1999). This may result from an enzyme deficiency or reduced enzyme activity.
Salicylates, found in foods with artificial dyes, food preservatives, flavorings, sweeteners, are a natural plant toxin found in most stone fruits, berries, citrus fruits, some vegetables, honey, yeast extracts and almonds.  Dr. Benjamin Feingold (1975) reported that foods and additives containing high salicylates can cause hyperactivity in children.  Salicylate sensitivity can result in headaches, lack of concentration, breathing problems, hyperactivity, electrolyte abnormalities, gastrointestinal problems.  Studies by the American Academy of Pediatrics (2008) support the idea that a wide variety of chemicals can results in neurobehavioral toxicity and some children will benefit from a preservative-free, food coloring-free diet.
The Feingold Diet prohibits foods containing naturally occurring and synthetic forms of salicylates, for example berries, stone fruits, citrus fruits, except for lemon, certain apples, almonds, cucumber, tomato, peppers, yellow, red, blue and other dyes.
Oxalate, a highly reactive molecule that is abundant in many plant foods.  When in human cells in high amount, oxalates can lead to oxidative damage, depletion of glutathione, ignition of the immune systems inflammatory cascade and the formation of crystals which seem to be associated with pain and prolonged injury (Owens).  When there is leaky gut, prolonged diarrhea or constipation, excess oxalate can be absorbed from the GI tract and become a risk to other cells in the body.  Oxalates are found in chocolate, soy bean, black bean, kidney bean, navy bean and pinto bean, sesame oil, blackberries, currants, dates, figs, oranges, raspberries, buckwheat, millet, rye, oregano, cinnamon, black pepper, almonds, cashews and other nuts.
Specific Carbohydrate Diet (SCD), pioneered by Gottschall, advocates the elimination of carbohydrates which require numerous digestive processes, resulting in an environment that supports overgrowth of intestinal yeast and bacteria.  SCD deprives the microbes in the intestine of the food they need to overgrow.  Pre-digested carbohydrates in the diet can maximally nourish the individual without over-stimulation of the intestinal microbial population.
GAPS (Gut and Psychology Syndrome) Diet prohibits all grains, gluten, casein and corn, phenol and salicylate containing foods.  It prohibits starchy vegetables and food produced from them, sugar, starchy beans, lactose and lactose containing foods such as milk, dried milk, yogurt and sour cream.