Restoring a healthy gut?

It’s becoming more apparent that my gastrointestinal system is about as healthy as my mental health. Clozapine has worsened already problematic constipation and the high protein diet that I’m using to combat weight gain certainly hasn’t helped that, nor the excessive (highly malodourous) flatulence. A month on a general probiotic initially seemed promising but it seems I need to further modify my diet. Even on the high protein diet, once again, I’m gaining weight. Food cravings are extreme and I wake up in the middle of the night – essentially on autopilot aka ‘clozapined’ – to eat…

I would say I’ve never really had a well functioning GI system and with all the research pointing to the role of the microbiome and brain-gut axis in health and illness, it’s time to see if I can change that with some simple and safe dietary modifications.

Basically, I’m considering continuing the probiotic and adding prebiotics, additional soluble fibre and enriching my diet with polyphenols to align with a more ancient and traditional one:

“Comparisons of the modern Western-style diet (WSD) with more ancient and traditional diets are helping to redefine the paradigm of malnutrition. Malnutrition is no longer restricted to the lack of certain essential nutrients, but also encompasses over nutrition and aberrant nutrient ratios and profiles. The WSD is typified by altered fat profiles with elevated saturated fats and synthetic trans-fatty acids compared to essential fatty acids and unsaturated fatty acids (mono- and polyunsaturated) and low availability of saturated fats in more traditional diets. The WSD is also defined by high levels of refined carbohydrates or sugars as opposed to traditional diets where foods enriched with complex, lowly digestible highly fermentable carbohydrates (e.g., fiber and prebiotics) form staples and support a saccharolytic, SCFA-producing gut microbiota. For proteins too, major differences occur between WSD and more traditional diets and foods, with amino acid composition and profile of foods being altered by industrial food-processing technologies. The WSD has largely replaced plant polyphenols as preservatives and to a lesser extent flavorings with chemical substitutes and finally, modern foods have substituted the phylogenetically diverse and numerically dense microbial food passengers found on traditional fermented and raw foods with monocultures of strains selected for technological purposes or more commonly, with sterility. Within the human “super-organism,” nowhere are the metabolic consequences of this altered nutritional environment more obvious than in the interactions between the gut microbiome and host energy metabolism and brain function. We have known for a while now that the gut microbiome and its interactions with diet plays a critical role in energy homeostasis and immune tolerance. We have linked aberrant gut microbiota profiles with diseases of immune function or autoimmune diseases and metabolic diseases like obesity, diabetes and non-alcoholic fatty liver disease. However, only very recently has altered brain development been considered a consequence of our closely co-evolved gut microbiome being out of step with our modern diet.” [1]

1. The probiotic

I’m using a clinically tested 26 billion CFU probiotic (Bifidobacterium lactis HOWARU HN019 5 billion CFU, BI-04 10.5 billion CFU; Lactobacillus acidophilus La-14 10.5 billion CFU).

“There are some studies showing effects of probiotics on brain function in healthy humans. For example, women who had taken a fermented milk product containing four probiotics (Bifidobacterium animalis subsp. lactis, Streptococcus thermophiles, Lactobacillus bulgaricus, and Lactococcus lactis subsp. lactis) showed reductions in brain responses to an emotional task, particularly in sensory and interoceptive regions that were measured with functional magnetic resonance imaging. Moreover, in another study, global psychological distress and anxiety symptoms, as measured by the Hospital Anxiety and Depression Scale, were improved in the group taking a Lactobacillus and Bifidobacterium-containing probiotic compared with those taking a matched control product. Importantly, probiotic supplementation of the mother during and after pregnancy has been shown to alter the infant’s microbiota. There is a need for future trials focusing on the best combinations of probiotic strains, the timing of administration, and whether these probiotics are more efficacious in conjunction with prebiotics. Also the mechanisms of action of probiotics are understudied and further investigating why certain bacterial strains have positive effects on brain health will be an important area into the future.” [1]

Recently, a randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood provided “…the first evidence that the intake of probiotics may help reduce negative thoughts associated with sad mood” [2]

Gut microbiota modulation and implications for host health: Dietary strategies to influence the gut–brain axis
Gut microbiota modulation and implications for host health: Dietary strategies to influence the gut–brain axis

2. The prebiotic

“Prebiotics are nondigestible food ingredients that selectively stimulate the growth of probiotic bacteria such as Lactobacilli and Bifidobacteria in the gut. Increasing the proportion of these bacteria with prebiotics such as galactooligosaccharides or fructooligosaccharides has many beneficial effects on the gut, the immune system, and on brain function, specifically, increased BDNF expression and NMDA receptor signaling, providing initial support for further investigations of the utility of prebiotics in mental health and potential treatment of psychiatric disorders. Recently, a human study has shown that subjects supplemented with galactooligosaccharides displayed a suppression of the neuroendocrine stress response and an increase in the processing of positive versus negative attentional vigilance, showing an early anxiolytic-like profile. Inulin-type fructans and lactulose modulate gut transit, decrease putrefactive activity within the gut lumen, prevent GI infections, and mitigate inflammatory responses” [3]

I’m using inulin:

“Inulin and oligofructose are considered as functional food ingredients since they affect the physiological and biochemical processes in rats and human beings, resulting in better health and reduction in the risk of many diseases. Experimental studies have shown their use as bifidogenic agents, stimulating the immune system of the body, decreasing the pathogenic bacteria in the intestine, relieving constipation, decreasing the risk of osteoporosis by increasing mineral absorption, especially of calcium, reducing the risk of atherosclerosis by lowering the synthesis of triglycerides and fatty acids in the liver and decreasing their level in serum. These fructans modulate the hormonal level of insulin and glucagon, thereby regulating carbohydrate and lipid metabolism by lowering the blood glucose levels; they are also effective in lowering the blood urea and uric acid levels, thereby maintaining the nitrogen balance. Inulin and oligofructose also reduce the incidence of colon cancer.” [4]

Even at doses as low as 2.5 g twice a day, inulin can exert a prebiotic effect in healthy volunteers by stimulating bifidobacteria growth. [5] Doses of 5-40g have been used for therapeutic purposes: 10 g per day for lowering triglycerides to upward of 40 g per day for relieving constipation. It has been reported that prehistoric foragers in the Chihuahuan Desert ate a diet which contained upward of 135 grams of inulin-like fructans [6].

“An inulin dose of 5–8 g/d should be sufficient to elicit a positive effect on the gut microbiota. One possible side effect of prebiotic intake is intestinal discomfort from gas production. However, bifidobacteria and lactobacilli cannot produce gas as part of their metabolic process. Therefore, at a rational dose of up to 20 g/d, gas distension should not occur. If gas is being generated, then the carbohydrate is not acting as an authentic prebiotic. This is perhaps because dosage is too high and the prebiotic effect is being compromised, i.e., bacteria other than the target organisms are becoming involved in the fermentation.” [7]

In overweight adults, treatment with galactooligosaccharides induced “favorable” changes in gut microbial composition, increased secretory IgA levels, and reduced inflammation and measures of the metabolic syndrome [8]

10g of inulin tastes fine mixed in with a protein shake.

3. Polyphenols etc:

I’m using raw cocoa [cacao] powder. It is known to be rich in polyphenols, such as catechin, epicatechin, procyanidin B2 (dimer), procyanidin C1 (trimer), cinnamtannin A2 (tetramer), and other oligometric procyanidins [9] It has numerous health benefits and provides caffeine and theobromine [10]. I’m using a dose of 30g/day [380kJ, 6.4g protein, 7.6g carbohydrate]

“Cocoa is a food relatively rich in polyphenols, which makes it a potent antioxidant. Due to its activity as an antioxidant, as well as through other mechanisms, cocoa consumption has been reported to be beneficial for cardiovascular health, brain functions, and cancer prevention. Furthermore, cocoa influences the immune system, in particular the inflammatory innate response and the systemic and intestinal adaptive immune response. Preclinical studies have demonstrated that a cocoa-enriched diet modifies T cell functions that conduce to a modulation of the synthesis of systemic and gut antibodies. In this regard, it seems that a cocoa diet in rats produces changes in the lymphocyte composition of secondary lymphoid tissues and the cytokines secreted by T cells. These results suggest that it is possible that cocoa could inhibit the function of T helper type 2 cells, and in line with this, the preventive effect of cocoa on IgE synthesis in a rat allergy model has been reported, which opens up new perspectives when considering the beneficial effects of cocoa compounds. On the other hand, cocoa intake modifies the functionality of gut-associated lymphoid tissue by means of modulating IgA secretion and intestinal microbiota.” [11]

4. Supplemental dietary fibre

NOTE: In case of medication-induced constipation, caution is required when increasing fibre intake.

“Dietary fibers pass through the upper intestine and are fermented by large-bowel anaerobic microbiota to produce SCFAs. SCFAs promote gut epithelial integrity and exert immune effects, including stimulation of G protein–coupled receptors, promotion of innate (Toll-like receptor 2) immune responses, and induction of regulatory T cells” [8]

I’m sticking with psyllium husk in divided doses. I’ve found it has better effects for alleviating constipation when it’s mixed with water and a macrogol 3350 sachet.

I’ll see how it goes!

See also:

A role for the microbiome in schizophrenia?

Dietary glycemic index as a modulator of behavioral and biochemical abnormalities?

Immunomodulatory Effects of Probiotic Supplementation in Schizophrenia Patients: A Randomized, Placebo-Controlled Trial.

The gut microbiota and inflammatory noncommunicable diseases: Associations and potentials for gut microbiota therapies

Gut microbiota modulation and implications for host health: Dietary strategies to influence the gut–brain axis

Host microbiota constantly control maturation and function of microglia in the CNS


3 thoughts on “Restoring a healthy gut?

  1. After some concerning issues (Note to self: don’t dramatically increase bulk forming fibre intake when dealing with medication-induced constipation), I’m happy with the initial changes that a prebiotic/probiotic/fibre combination have brought about. For once in many years, I’m ‘regular’. That’s with the help of standard doses of lactulose and macrogol…

    Frequency and malodorous nature of wind have resolved (it seems the combination enhances motility and prevents putrefaction, particularly important on the high protein diet). The cacao makes for a nice drink. I’ve added some other raw food products temporarily.

    I also have some digestive enzymes which I’ll play with at a later date and see what they have to offer.

    Goal for now: lose most of those 7kg I put on in a month thanks to late night clozapine feasts. I’m happy to say coming off the clozapine has so far gone OK (now at 150mg) – I’m looking forward to being totally off it.


  2. Update: The inulin still really seems to be helping with the constipation and wind issues. I’m using that at about 30g/day with my protein shakes (twice daily). I also use about 10g with my macrogol sachets (2-3) at night.

    I’ve trialled several different probiotics including a broad spectrum one but haven’t noticed much difference. For now, I’ve settled on a 100 billion CFU version of the one originally mentioned in the post.

    Weight is still something I’m paranoid about. It’s been fluctuating and I’d like it to drop a bit. I feel full and in control of my appetite during the day but post-clozapine ‘night feasts’ are still an issue (clozapine now at 100mg). The protein/inulin seems to be perfect for keeping food cravings at bay during the day.

    Hopefully the GI issues will be less of a problem as the clozapine dose continues to decrease.

    I’m still using the raw cacao/cocoa powder at 30g/day. I don’t notice much from it but the fibre intake it provides seems to be beneficial. I’m battling caffeine addiction at the moment so it’s hard to notice anything in the way of theobromine effects etc. I’m hoping the antioxidant effects of the flavanols are beneficial, likewise the potential immune benefits mentioned in the post. A recent article ‘The effect of flavanol-rich cocoa on cerebral perfusion in healthy older adults during conscious resting state: a placebo controlled, crossover, acute trial.’ ( provides a mechanism for some potential cognitive benefits

    After the initial troubles with psyllium husk, I’ve stopped using that.


  3. Nearing the end of my clozapine days, I have now stopped my protein shakes and gone back to a normal diet. Still using the cacao at 15g and the inulin at 10g/day with my probiotic. In general, gut health is much better.


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