A Bioenergetic Approach to Restoring Gut Function: Part 2

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Oops - A bioenergetic approach to restoring gut function part 1 was almost two years ago, my studies got the better of me, I’m sorry. Following on from the information of how to restore energy and digestion by simply removing foods that are difficult to digest, promote endotoxin, decrease energy and digestion. Replacing them with easily digested, protective nutrients can negate the need for expensive, reduced testing and a supplement list that causes you to rattle as you stroll down the street. Much like the decreased need for stool testing, I have rarely recommended a food allergy or sensitivity test for the same reason that I haven’t used a stool test for many years (or had the luxury of a nice cash kickback from the labs I used to use). Why? Because these tests show the body in a stressed, energy wasting state that is prone to inflammation and reacts with many foods like dairy. Is it the food? No. Could it be you? It’s possible.


It’s not the dairy it’s you

Elie Metchnikoff suggested over 100 years ago that as putrefaction within the bowel occurs, function and immunity is compromised


Many clients have rolled into the office clutching their food sensitivity tests in a file, with dozens of other tests. Red bars, yellow bars, all highlighting so called problem foods. During bouts of stress (pollution exposure, psychological, under eating etc, excessive exercise, poor sleep) the body is prone to decreasing available levels of organisational hormones such as thyroid and progesterone. Usually the adrenal glands have to pick up the slack and compensatory stress hormones such as cortisol, glucagon, adrenaline and activation of serotonin (not a hormone) which  suppress thyroid and progesterone are perpetuated. This often creates a high sodium (salt) and magnesium wasting state and poor digestive function that facilitates increased sensitivity via increased serotonin and histamine levels. This also increases demand for vitamin C for gut mucosa maintenance and adrenal responses.

If this state is perpetuated increases in endotoxin (the by-product of bacterial metabolism and degradation ) burden the digestive system, liver, and can damage the gastrointestinal lining. Endotoxin levels are also  increasing through airborne environmental pollutants such as polycyclic aromatic hydrocarbons  from fossil fuel use and industry (Annamalai & Namasivayam, 2015), so it’s worth considering that some people in a high pollution area, with poor digestive function are at increased risk of presenting with food sensitivities. They get tested, part with their cash and told to cut out 20 foods that they eat on a regular basis. Problem solved? Well no, it’s an intervention that will have some success but it’s some distance of what the person really needs.

 To simplify some of the well-known digestive issues with two ends of the spectrum.

Your bowel function might be an expression of your biology.jpg

Restore function

Restore appropriate movement

Constipation – failure to go to poop daily, hard to pass.


IBS irritable bowel like issues. Loose often more than 3 times per day.


There’s plenty of reasons to link constipation with a low energy, functionally hypothyroid, subclinical or overt hypothyroid state (Lauritano et al., 2007) and increased bacterial overgrowth like SIBO or small intestinal bacterial overgrowth. The digestive system is energy and thyroid hormone dependant and restoring energy by supplying easily digested high energy foods can be a simple intervention with effective results.

Often when you dig into a person’s history, you might find that those with IBS like states often describe a period of constipation. It’s not impossible to suggest that sustained constipation will lead to increased endotoxin, serotonin and histamine that damages the bowel lining. When this environment is perpetuated by stress, poorly digested foods and low energy, the digestive system is maintained in a high stress state, sensitive and ready to reject any remotely objectionable substance. Any food can become problematic when the digestive system is over-burdened or sustains damage to enzyme producing structures in the villi and microvilli.

 If you follow the chart suggested in restoring gut function part 1, you should find yourself in a much improved state. If you need further improvement then the following factors have always worked well:



 Magnesium in forms such as chloride and glycinate or very useful for decreasing perceived stress and lowering the incidence of sensitivities and 400mgs to 1g is useful to experiment with and complements dietary changes suggested.

To restore bowel movement magnesium sulphate or Epsom salts will mobilise the digestive tract and I have found that clients if needed try half to a full teaspoon to grease the wheels.

Vitamin C is a great way of decreasing constipation. A few years back I would recommend a dose of 1-2 grams  but equally I feel adequate intake of orange juice will do a great job. The added benefit of orange juice (polyphenols) has been shown to decrease inflammation and endotoxin which is often present in both high fat and carbohydrate meals (Ghanim et al., 2010).


Cascara Sagrada If you need a good clear out to restart function then cascara is an extremely effective solution.

‘ An effective laxative (besides preventing inflammation) causes not only coordinated contraction of the smooth muscles of the intestine, but also adjusts secretions and absorption, so that an appropriate amount of fluid stays in the intestine, and the cells of the intestine don’t become water-logged.’ Ray Peat.


Caffeine seems a logical choice and the research on caffeine as a potent factor in the fight against cancer and neuro degenerative diseases such as dementia and Alzheimer’s disease is very positive. Coffee stimulates bowel function and like the suggestions above is useful to decrease the reabsorbed metabolites and toxins that may be instrumental in systemic inflammation. The aerobic/respiratory system is enhance and protected by coffee consumption, providing protection to the mitochondria (Eskelinen & Kivipelto, 2010).


Irritable bowel

Carrots I have posted about the power of grated carrot to reduce the irritated state many times and have seen some clients with over 20 years of IBS resolve with this simple addition. Carrots act as a natural antibiotic, lowering endotoxin and other bacterial end products (Babic, Nguyen‐the, Amiot, & Aubert, 1994) and bamboo shoots have the same effect. As increased bacterial issues stimulate endotoxin production the daily use of a carrot salad can be one of the simplest yet most effective tools that you can have to improve bowel function.

Bone broth, gelatin and glycine are also great for helping to support gastrointestinal mucosa, improve the brush border enzyme function and decrease the proinflammatory effects of eating tryptophan and iron rich muscle meats that can also irritate the bowel when excessive.

Mushrooms  when boiled also have a similar effect as the carrot by decreasing aromatase enzymes and estrogen  acting as a natural antibiotic.

I would challenge anyone who either has paid money for a food sensitivity test or who is thinking about it ,to simply try the suggestions set out in these two posts. Over the last few years I haven’t seen anyone who has failed to improve digestive function. Although sometimes other mechanisms involving hormones may need to be explored.


Annamalai, J., & Namasivayam, V. (2015). Endocrine disrupting chemicals in the atmosphere: Their effects on humans and wildlife. Environment International.

Babic, I., Nguyen‐the, C., Amiot, M. J., & Aubert, S. (1994). Antimicrobial activity of shredded carrot extracts on food‐borne bacteria and yeast. Journal of Applied Bacteriology.

Eskelinen, M. H., & Kivipelto, M. (2010). Caffeine as a protective factor in dementia and Alzheimer’s disease. In Journal of Alzheimer’s Disease (Vol. 20).

Ghanim, H., Sia, C. L., Upadhyay, M., Korzeniewski, K., Viswanathan, P., Abuaysheh, S., … Dandona, P. (2010). Orange juice neutralizes the proinflammatory effect of a high-fat, high-carbohydrate meal and prevents endotoxin increase and toll-like receptor expression. American Journal of Clinical Nutrition.

Lauritano, E. C., Bilotta, A. L., Gabrielli, M., Scarpellini, E., Lupascu, A., Laginestra, A., … Gasbarrini, A. (2007). Association between hypothyroidism and small intestinal bacterial overgrowth. The Journal of Clinical Endocrinology and Metabolism, 92(11), 4180–4184.

 Peat, R.

Better gut health with less bacteria?

Can you have better gut health with less bacteria? There’s an old saying in the integrative health world that ‘ Death begins in the colon.’ These were the words of the 1906 Nobel science award holder Elie Metchnikoff, a Russian scientist who did much to elaborate on the mechanisms of embryology, immunology and other aspects of health and disease. These days there’s much that has been written about the micro biome and the suggestion that diverse microbes within the bowel are an important factor in health. How we need to eat plenty of fibrous and fermented foods for better health. But how true is this and are more bacteria necessary for better digestion and longer life? “The retention of faecal matter for several days very often brings harmful consequences. Organisms which are in a feeble state from some cause are specially susceptible to damage of the kind referred to.” (Metchnikoff & Metchnikoff, 1908)

Ok so you aren’t likely to die anytime soon from being constipated for several days, you might feel like crap (excuse the pun). But what if the repetition of constipation is over years? We have seen that hypothyroidism and constipation is clearly linked and can induce small intestinal bacterial overgrowth (Lauritano et al., 2007). An inability to remove the waste products is a particular burden on a stressed system.

"Not only is there autointoxication from the microbial poisons absorbed in, cases of constipation but microbes themselves may pass through the walls of the intestines."

This description of endotoxin and other bacterial end products damaging and permeating the intestinal wall is a well-known modern concept of leaky gut or intestinal hyper permeability. Metchnikoff’s describes the putrefaction (think fermenting mass of stinky stuff) of foods within the bowel that lead to the damage described in a permeable gut lining that allows bacteria and endotoxin into the blood stream.

There’s a theory that I have, as it’s clear that not all people have constipation. Many present with irritable bowel syndrome (IBS) like states, loose and perhaps a product of irritation induce by high serotonin and histamine (which by keeping to a minimum can also improve sleep and mood). It’s plausible to suggest that some people have already gone through a constipated phase induced by either a low energy or thyroid state, which may give way to a high adrenaline state over time. The lack of movement in the bowel for some can set the scene for future IBS reactions due to the accumulative damage induced by constipation, putrefaction, bacterial end products and increased irritation. Some clients have noticed that they previously went through a constipated phase before they arrived at their suggested IBS.

So if the current theme of recommending probiotics, raw and fermented foods is in vogue. What does that mean for the digestive system. I remember a newsletter from Ray Peat suggesting that animals born in a sterile environment generally live longer and have a higher metabolic rate. This in itself is a hard, near impossible feat to achieve outside of a sterile laboratory but consider this - Most babies are grown within a womb that does not contain any bacteria, as soon as they come through the birth canal and into the world at large. The bacterial management of life comes into play and had it come any sooner, may have had disastrous consequences. Other observations of Metchnikoff related to the longevity of birds, which have a high metabolic rate and limited intestinal flora -

‘Even in birds of pray which feed upon putrid flesh, the number of microbes in the intestine is remarkably limited. I have investigated the case of ravens which I fed flesh which was putrid and swarming with microbes. The droppings contained very few bacteria, and it was remarkable that the intestines had not the slightest smell of putrefaction. Although the opened body of a herbivorous mammal, such as a rabbit, gives off a strong smell of putrefaction, the body of a raven with its digestive tube exposed has no unpleasant smell. The absence of putrefaction in the intestine is probably the reason of the great longevity of such birds as parrots, ravens, and their allies.’

Metchnikoff also states that despite the absence of bacteria, their organisation and metabolism may be the primary driver for long health. Therefore if we were to keep bacterial interference at bay might we be better at living longer lives by improving our gut health? Our metabolism and cellular health is the key to prevention of many disease states. Extra bacteria may just be another factor that our immune system has to contend with and may be at the heart of autoimmune issues. From a comparative biology standpoint many other herbivorous animals don’t live as long as omnivorous animals. Horses, cows, and sheep live very short lives in comparison to other mammals that eat a wide range of foods. The main exception being the elephant, which has an extremely large intestine like other vertebrates.

Probiotics and fermented foods provide a mixed bag of research(Goldenberg et al., 2015). In many studies bacterial infections and digestive issues have not been resolved by probiotics. They do seem to be particularly effective at reducing bacterial/food poisoning cases and decreasing the diarrhoea like state by a day or two. Primarily this acts as a competing organism in the battle of the bowel and maybe why faecal implants have been shown to beneficial in the short term for some.. Even beneficial strains of bacteria such as lactobacillus can be problematic in excess due to the high levels of lactic acid leading to d-lactate acidosis, decreasing our gut health and overall wellbeing.

After all increased bacteria equals increased immune system responses and constant battles, for some there’s only so much that a faltering metabolism and immune system that one can take. Providing easily digested nutrients that limit bacterial growth and metabolites, that doesn’t burden a compromised digestive system seems prudent. In hypothyroidism gastric secretions such as hydrochloric acid are often lowered, further compromising digestion. Easily digested nutrients equals easily available source of energy and macronutrients.

To read more on how to combat these issues, to improve your gut health, digestion, mood and energy, this article is extended in the members’ area or there's also some information in this blog from 2017.


Goldenberg, J. Z., Lytvyn, L., Steurich, J., Parkin, P., Mahant, S., & Johnston, B. C. (2015). Cochrane Database of Systematic Reviews. The Cochrane database of systematic reviews (Vol. 12).

Lauritano, E. C., Bilotta, A. L., Gabrielli, M., Scarpellini, E., Lupascu, A., Laginestra, A., … Gasbarrini, A. (2007). Association between hypothyroidism and small intestinal bacterial overgrowth. The Journal of Clinical Endocrinology and Metabolism, 92(11), 4180–4184.

Metchnikoff, E., & Metchnikoff, I. I. (1908). The Prolongation of Life: Optimistic Studies. Our post human future. Consequences of the biotechnology revolution. Retrieved from

An energetic approach to restoring gut function: Part 1.

Let’s kick this blog off with a question as to whether or not an energetic approach to restoring  gut function is useful or should we rely on testing and supplements? Let me clarify, that I have had my fair share of success stories with a reduced and diagnostic approach to improving gut health. Just like I have also had my fair share of kickbacks from the laboratory for recommending their tests. At one point I was using nearly 200 stool tests per year and making a little cash on the side. Many of the tests worked in isolating some specific disturbance to their gut bacteria, presence of a parasite or elevation of putrefied fatty acids. A ‘cleansing’ diet was promoted and a few supplements for good measure created some short term change whilst the client was in my care. But here’s why the long-term approach to that type of assessment and treatment may not be the best response. A standard functional medicine approach  after spending quite a lot of cash on an integrated stool test is using the 4 R approach.

Remove (offending parties)- spend money on supplements

Restore function- spend money on supplements

Re-inoculate - spend money on nice expensive probiotics

Repair gut lining- spend money on supplements

Regurgitate. Ok the 5th one is mine but no supplements needed.

By taking this approach, an important question is not asked of the individual. Why is this person experiencing an overgrowth of bacteria/SIBO, parasitic infection, endotoxin overgrowth, inflammation and degradation of the bowel lining? I like to think that it is not because of the easy kickbacks FM practitioners are getting for the lab tests and supplements they recommend? So what is the persons level of biological energy and immune system function that allows their digestive system to get in such a state. We know there are some usual suspects. Food, stress or alcohol perhaps?

The typical gastrointestinal complaints people came to me with, were bloating, excess gas, constipation or irritated loose stools combined with poor energy. It was Ilya Mechnikov who originally stated that death starts in the bowel or colon and there’s’ certainly many degenerative and inflammatory conditions that appear at the last stop to poopy central. But is the bowel the main driver of this dysfunction? Many of the symptoms that I recalled earlier are also key symptoms of an energetic and perhaps a thyroid dysfunction. So instead of reaching for our drastic 4 R protocol with an expensive poo test lets consider the following.

 The likes of Broda Barnes and Ray Peat have highlighted how a lack of energy, either from a low or inappropriate food intake or a dysfunctional hypothalamic-pituitary-adrenal-thyroid axis can be evaluated by assessing body temperature and the combination of pulse. Additional information on Thyroid and TSH evaluation can be found here.

Most people are aware that when they get stressed or exercise, blood is shunted away from the digestive system to the periphery and other working tissues. Even the concept of high Adreno-corticotrophic hormone (ACTH), cortico releasing hormone (CRH) and adrenal production of cortisol is becoming common place in work and gym environments alike. These hormones suppress thyroid hormone and the energy compound ATP that provide energy for tissues.

It’s also well known that low energy states create tight painful muscles that are difficult to relax and one might be able to apply that line of thought to the smooth muscle tissues that regulate bowel contractility. Therefore a low energy state that does not allow for adequate energy production will not allow adequate digestion and bowel function to occur. Cold hands and feet can be a symptom of not eating enough carbohydrate and protein.

If the cold hands and feet, low body temperature, fatigue, constipation don’t resolve from eating energy rich meals that contain plenty of fruit and contains little of the foods that promote the bowel irritants histamine and serotonin (nuts, seeds, vegetable oils, grains, gluten free products, beans and pulses). Then, often factors that influence the hormones such as thyroid, estrogen and progesterone may need a deeper consideration.

I drafted a little flow chart that will be helpful for some quick strategies on what might be happening but what I would like to focus on the low energy state that might have its source from a food or hormone factor or perhaps both. Instead of using a strategy like the 4 R approach, these simple questions can help guide you to understanding whether it is the foods that you eat or an energetic factor that could be causing your digestive system to suffer. It's not a complete algorithm but it does offer some simple solutions that have helped plenty of people resolve digestion and energy issues.

Foot note: I haven't needed a stool test with a client for over 4 years now following this chart.


In part 2 I will elaborate on foods and basic supplements that can be used to resolve most long standing digestive issues and understanding other hormone actions that create digestive discord.


Lokaj, J., & John, C. (2008). [Ilya Ilich Metchnikov and Paul Ehrlich: 1908 Nobel Prize winners for their research on immunity]. Epidemiologie, Mikrobiologie, Imunologie : Casopis Spolecnosti pro Epidemiologii a Mikrobiologii Ceské Lékarské Spolecnosti J.E. Purkyne, 57(4), 119–24. Retrieved from

Peat, R. (1997). From PMS to Menopause: Female Hormones in context.

Peat, R. (2006). Autonomic Systems. Retrieved from