Digestion and Nutrition

One of the most impactful changes that clients of Dr Brogan make for whole-body and mind health is to improve their diet and digestion. Elimination of suspected or confirmed food sensitivities, followed by the addition of probiotics and supporting parasympathetic tone were mainstays of protocols to regularize digestion, provide gut relief from inflammatory foods, and support the immune system through the microbiome. Vitamin and mineral supplementation (such as iron, methylated and activated B vitamins, and vitamin D3) was also consistently used to promote stable mood by providing cofactors for neurotransmitter and hormone synthesis, as well as increasing nutritional status to allow other physical healing processes to take place. The basis for the dietary recommendations presented in this case series is to promote a healthy gut microbiome and decrease systemic inflammation, ultimately promoting increased levels of energy, mood, and cognition. The diet aids with symptoms of withdrawal throughout the taper, as well as enhances general well-being. For this reason, the prescribed diet is continued post-taper. While the diet has many components, most importantly it is free of gluten and dairy, and it is low glycaemic. Gluten is a protein found in wheat that increases systemic inflammation and promotes intestinal permeability (also known as leaky gut). These processes occur through the stimulation of gut and liver cells to release more Zonulin. Zonulin is a normally occurring protein synthesized by liver and intestinal cells that regulates the permeability of the intestine. It is believed that gliadin (a protein found in wheat, rye, and barley) has the effect of triggering Zonulin activity and causing increased gut permeability. (8–12) Because serotonin in the brain and retina is synthesized under the control of a circadian clock, we sought to determine if a circadian clock in the duodenum regulates serotonin synthesis and release in blood. We examined gene expression in the duodenum of chickens at different times of the day and found that the duodenum rhythmically expresses molecular circadian clock genes and genes controlling serotonin biosynthesis, specifically tryptophan hydroxylase, in a light dark cycle (LD Because of increased permeability, undigested food particles, bacteria, and other larger molecules are able to pass through the gut lining and enter the bloodstream. These foreign bodies elicit an immune response, and the inflammatory cascade that follows leads to many unwanted ‘allergic’ reactions such as Irritable Bowel Syndrome (IBS), chronic fatigue, migraines, eczema, and others. (7) Furthermore, a phenomenon known as hyper-excitable celiac brain may explain some of the neurological effects of gluten-mediated systemic inflammation. Many studies have explored cytokine activity on the blood-brain barrier (BBB) and observed that binding of these molecules increased paracellular permeability and thus disrupted the barrier. (13) Oxidative stress, such as glyco oxidative stress from a high glycemic diet or diabetes, can further this barrier break down. This notion is demonstrated in the use of antioxidant alpha-lipoic acid for repair of the BBB. (7) In another study, researchers found gluten to play a role in mood changes for both celiac and non-celiac sensitive patients during a blinded gluten-free diet vs. placebo trial. (14) Results showed an increase in mood when gluten was eliminated from the diet. The study also noted a worsening of symptoms when non-celiac patients were introduced to gluten. However, it should be noted that gluten can have negative consequences even for those without explicit intolerances or celiac disease. The aforementioned process of zonulin increasing gut permeability can lead to a cascading immune response in 80% of the population based on hereditary haplotypes. (12) Additionally, lipopolysaccharides (from bacterial cell walls) can enter through a permeable gut and have been linked to depression.(15) 

A 2014 study published in the journal Brain, Behaviour and Immunity concluded that there was a correlation between raised inflammatory markers and MDD.6 This was exhibited in a trial where patients’ IL-6 and IL-10 levels were lowered after an 8 week treatment period with Sertraline.6 The inflammatory effects and mood changes associated with consuming gluten are why the prescribed diet calls for its elimination. Dairy is another product that patients are asked to remove from their diet. While those with lactose intolerance  


Several strategies were used to optimize clients’ detoxification pathways, focusing on the enhancement of liver function, hydration, effective digestion, and elimination, as well as the function of the skin as an emunctory organ. As such, daily dry-skin brushing and coffee enemas were recommended to these patients. Dry-skin brushing increases lymph drainage, encouraging optimal circulation of functional immune cells and cytokines, and transportation of inflammatory debris for elimination. Coffee enemas promote detoxification of hormones, toxins, and other metabolites by the liver. (20)

Coffee Enemas

Coffee enemas were recommended daily in the mornings, using freshly brewed organic coffee brought to body temperature. With a few basic pieces of equipment, coffee enemas can be done at home as a 25-minute process, ideally after a morning bowel movement. The coffee is thought to stimulate the sacral parasympathetic nerve plexus in the colon, then reflexively increasing bile secretion and dilating hepatic ducts for more efficient bile flow and removal of toxicants.21 A secondary therapeutic effect of coffee enemas is an increase to peristaltic forces for effective elimination. (22) Coffee Enemas and Glutathione Glutathione is a highly potent endogenous antioxidant, and is ubiquitous in healthy human tissues as L-glutathione (GSH), accounting for about 90% of the body’s glutathione pool, the other 10% being the oxidized disulfide form (GSSG). (23) Coffee enemas induce the release of Glutathione S-transferases (GST), (22) the enzymes responsible for using glutathione to conjugate endogenous hormones such as estrogen, exogenous electrophile substances including many xenobiotics, and for reducing organic peroxides. (24,25) The catalyzation of GST requires palmitoleic acids, which are found in high amounts in organic coffee as diterpenes kahweol and cafestol palmitate, part of a proposed mechanism linking coffee enemas to enhanced detoxification. (22,23,26). This conjugation facilitates their removal from the body and plays a major role in cellular detoxification functions. Sufficiently available GSH and GST are necessary to keep up with the detoxification demands of the cellular debris of inflammation, turnover of hormones, and processing and excreting environmental pollutants. (27) Chronic neuroinflammatory states, including pain, cognitive decline, sequelae of traumatic brain injuries, and many psychiatric and neurologic disorders, are correlated with GSH deficiency or depletion. (28–30) Functional GSH deficiency has many causes. Genetic polymorphisms in the conjugating enzyme GST results in low GSH levels. (31,32) Nutrition is also crucial, as GSH production will be adversely affected by a diet insufficient in the amino acid precursors for GSH: cysteine, glycine, and glutamate. Likewise, inadequate intake of nutrient cofactors for glutathione synthetase will result in deficient GSH recycling. Finally, GSH depletion simply occurs because demand for antioxidant activity outweighs GSH supply due to excess oxidative stress, such as toxicant and xenobiotic load. Numerous studies have confirmed the immunoregulatory roles of GST and GSH. (33) In fact, increasing the levels of these inherent antioxidant compounds has been a developing focus for the field of nutrient supplementation, be it via optimizing nutrition for the production and function of GST and GSH, or supplementing with their bioavailable forms directly. Plasma GST levels increase after one coffee enema by up to 600-700% according to the Gerson Institute. (22,34,35) More research is indicated to clarify the mechanisms of glutathione potentiation following coffee enemas. (34,36)