After addressing the shortcomings of the allopathic treatment model, Dahlman declares, "IBS is simply a fundamental, functional deficit in 2 areas, bacteria and chemistry, and if not addressed, any other approach is doomed to failure." Each human being has many billions of friendly flora, beneficial bacteria in our gastrointestinal tract that, when kept in proper proportions, allow for a well-functioning digestive system. If the bacterial balance is in any way altered, typically through drugs or poor diet, the chemistry of the GI tract is altered and symptoms develop. These symptoms include pain and discomfort, bloating and abdominal distension, alternating diarrhea and constipation, abnormal bowel frequency or urgency, indigestion, GERD, and gas.

IBS is primarily caused by past or present antibiotic use. Antibiotics are used to kill microorganisms and can be useful for treating acute infections, but due to their nondiscriminatory nature, antibiotics kill all bacteria, including gastrointestinal flora. Dahlman quickly points out that "it doesn’t matter whether you’ve taken 2 or 200 courses in your lifetime. It also doesn’t matter if you took them all before you were 10-years old or throughout your life time. Each time you took them you destroyed a portion of the bacterial population and even though they are living, reproducing organisms, they don’t always reproduce back to proper proportions and in fact, they may reproduce to abnormal levels."

Other reasons why IBS develops in some individuals include NSAID use, complications of which have been linked to ulcers, bleeding and gastric damage, which are themselves a result of a change in GI chemistry. Poor dietary choices, specifically too much daily, fast food, processed food, and alcohol use are to blame for much the same reason. A lack of digestive enzymes ensures that the body is ill-equipped to break down food, resulting in malabsorption. Abnormal bacteria, parasites or yeast can also be factors. Stress, according to Dahlman, does not cause IBS, but can exacerbate symptoms.

In maybe one of the best examples of the holism of the human body, Dahlman explains how diet and drugs can act as a catalyst to a number of other diseases. Diet and drug use alter the level of bacteria in the GI tract, which affect the chemistry and lay the groundwork for IBS symptoms. Often, the intestines become unhealthy and inflamed, which causes them to expand and form microscopic "holes," through which microscopic, undigested matter enters the bloodstream, a phenomenon which is allopathically referred to as "Leaky Gut Syndrome." Once in the bloodstream, these undigested molecules are attacked by an ill-equipped immune system, which creates an antibody to the molecule and generates the production of histamine. Histamine, in turn, causes anything from headaches, pain, and skin rashes, to serious problems like asthma and anaphylactic shock. The reason that anti-histamines offer only short-term relief is that the body continues to produce histamine in response to the food that it can't break down and is therefore allergic to. Due to the body's inability to break down its protein, milk is the most common type of molecule to pass undigested into the bloodstream and provoke an antibody/histamine reaction. This can not only explain how a milk allergy is created, but also milk's role in the onset of allergies and asthma.

To address these issues, Dahlman offers a comprehensive solution that speaks to all of the causes of IBS as well as temporary dietary restrictions to allow the gastrointestinal system to utilize this treatment protocol. Persons looking to eliminate IBS should follow all suggestions, as each has an important role in healing. Two things must be done simultaneously, and both are temporary, with a typical treatment protocol lasting about 90 days.

Dietary restrictions need to be put into place which involve the complete avoidance of all dairy products (eggs and butter are fine, however). No milk, cheese, ice cream, sour cream, creamy salad dressings, yogurt, as well as any ingredients containing the following words in any context: milk (milk solids, milk by-products for example), cheese (cheese flavoring), lactose, whey and casein. These foods need to be avoided because they cause irritation of the gastrointestinal lining, and healing cannot begin until such irritation is stopped. Asthma, allergies to milk and skin problems will also improve once dairy is removed from the diet. And according to Dahlman, the avoidance of all dairy is a "100% rule." He is adamant that anyone attempting to eliminate their IBS symptoms completely eliminate dairy for the duration of treatment. "If you only eliminate dairy by about 85%, you might see no benefit at all." Most legumes (beans) need to be eliminated from the diet as well, the simple reason is that they cause gas, which needs to be minimized during treatment. Depending on the type of legume, they can also be difficult to digest. "Safe" legumes include green beans, peas and lima beans. All other beans, including black, red, refried, navy, kidney and garbanzo are out, as well as Mexican food and certain Indian and Middle eastern dishes and most soy products must also be eliminated.

In addition to restricting the diet, nutritional supplementation is a must when attempting to conquer IBS, and supplements fall into four distinct categories. Probiotics must be taken to restore the bacterial balance in the GI tract. Since the lack of proper numbers of intestinal flora is the root cause of IBS, probotics are paramount. Next, Dahlman recommends a liquid multivitamin and multimineral drink to heal the GI tract and to help with restoring chemistry. Thirdly, digestive enzymes are needed to help with proper digestion of foods. Lastly Dahlman suggests "a combination of peppermint, lavender and chamomile oils as it is anti-inflammatory, anti-gas and anti-spasmodic."

Dahlman states that a typical treatment protocol for Crohn’s Disease or Colitis would be similar in nature to this IBS treatment. He even suggests that Crohn's and Colitis may simply be an advanced form of IBS.