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Digestive imbalances in patents with chronic fatigue syndrome are common. For example, some studies suggest that up to 81% of patients have small intestine bacterial overgrowth and there is also a frequent co-morbidity between irritable bowel syndrome and chronic fatigue syndrome. If you haven’t already you may like to read our article on ‘Digestive Health & Chronic Fatigue Syndrome‘ which explores the research on digestive health in CFS, and our article series on ‘Small Intestinal Bacterial Overgrowth‘ which discusses the causes and effects of SIBO, as well as the testing and treating options.

This article is the next in the series on the topic of digestive health and offers some practical recommendations for restoring digestive health. While the title says ‘in chronic fatigue syndrome’ these recommendations are often going to be appropriate for many other conditions, or, for people who are in health and are seeking to maintain their health.

It is important to note that the below recommendations are generic, and factors such as the current health of your digestive system will partially dictate which of these will provide benefit, and which of these may in fact exacerbate symptoms. One approach is simple trial and error, the other is to start small (such as a teaspoon of sauerkraut per day) and slowly build. There are many reasons why people may react negatively to introducing some of these foods or products, and thus working alongside a practitioner, or simply being aware of this, is important.

The more diverse the diet, the more diverse the microbiome and the more adaptable it will be to perturbations……Today, 75 percent of the world’s food is generated from only 12 plants and five animal species

richness of the GI microbiome is well correlated with health


“when you don’t deliver enough of that stuff from plants, the bacteria have to eat something, so they start eating you….They eat your mucous lining in your colon, and it’s thought that maybe once you start to degrade that protective barrier, you then expose it to potential problems.” Jeff Leach

This quote in an interview with Chris Kresser falls in alignment with a fantastic paper that was published in 2016 that states:

Diets that advocate intermittent fasting may inadvertently establish occasional harvesting of the intestinal mucosal barrier by microbiota species that are capable of foraging on mucin glycans for fuel

Fibre is an essential component of our diet. Research has shown that fibre has the following health benefits:

  1. lowers the risk of cardiovascular disease
  2. improves blood sugar control
  3. improves regularity of bowel movements
  4. helps appetite control and thus body weight

Certain fibers, such as b-glucans, have been shown to interact with immune cells, and can therefore stimulate the immune system directly. Soluble, non-viscous fiber may also be potentially useful in alleviating symptoms of inflammatory conditions, such as irritable bowel syndrome (IBS). In particular, partially hydrolyzed guar gum has been shown to improve abdominal pain and bowel habits better than wheat bran and qualitative scores of epithelial injury and inflammation compared to control.

dietary fiber is protective against high CRP (inflammation) (Yunsheng, 2006)

Resistant Starch

Four main subtypes of resistant starch have been identified based on structure or source.

  1. Starch that is physically inaccessible to digestive enzymes is called resistant starch type 1 (RS1). RS1 is found in whole or partly milled grains and seeds so would be present in whole-grain foods.
  2. Starch that is resistant to digestion due to the nature of the starch granule is referred to as resistant starch type 2 (RS2); this type of resistant starch is found in raw potato, unripe banana, some legumes, and in high amylose starches such as starch obtained from high amylose corn.
  3. Resistant starch that forms from retrograded amylose and amylopectin during food processing is called resistant starch type 3 (RS3). This resistant starch form is found in cooked and cooled foods such as potatoes, bread, and cornflakes.
  4. The fourth type of resistant starch, resistant starch type 4 (RS4), is produced by chemical modification.

Health benefits in the large intestine include enhanced fermentation and laxation; increased uptake of minerals such as calcium; changes in the microflora composition, including increased Bifidobacteria and reduced pathogen levels; and reduced symptoms of diarrhea. Systemic effects involve plasma glucose and insulin, insulin sensitivity, and fatty acid oxidation.

Most early research on the health benefits of resistant starch focused on fermentation-related outcomes. Shortchain fatty acids, primarily acetate, propionate, and butyrate, are produced during resistant starch fermentation. They directly influence the large intestine environment, for example, by lowering intestinal pH, which inhibits the growth of pathogenic bacteria, increases the absorptive potential of minerals, and inhibits absorption of compounds with toxic or carcinogenic potential. Shortchain fatty acids also stimulate colonic blood flow, increase tone and nutrient flow, promote colonocyte proliferation, and reverse atrophy associated with lowfiber diets.

See our article on short chain fatty acid here.

Insoluble Fibre

Indeed, in some cases, insoluble fibres may worsen the clinical outcome.

The above quote is from a systematic review of fibre in irritable bowel syndrome. It has been shown that insoluble fibre may irritate an inflamed/irritable gut. Patients with irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), or other digestive disorders may benefit from reducing their intake of vegetables that are high in insoluble fiber. Vegetables, especially non-starchy vegetables tend to be high in insoluble fibre.

  • Peas, green beans, spinach, lettuce, kale, onions, leeks, cabbage, bok choy, brussel sprouts, broccoli, garlic, cauliflower

These food preparation steps can make non-starchy vegetables easier on the digestive system:

  1. Always eat insoluble-fiber foods with other foods that contain soluble fiber. Never eat insoluble-fiber foods on an empty stomach.
  2. Remove the stems and peels (i.e., from broccoli, cauliflower, and winter greens) from veggies (and fruits) high in insoluble fiber.
  3. Dice, mash, chop, grate, or blend high-insoluble-fiber foods to make them easier to break down.
  4. Eat well-cooked insoluble-fiber foods: steamed thoroughly, boiled in soup, braised, etc.; avoid consuming them in stir-fries, and if you do eat them raw, prepare them as described in #3 above

Soluble Fibre

Soluble fibre has been shown to be of more benefit that insoluble fibre in irritable bowel syndrome. Psyllium may be a beneficial supplement.

Sources include: Carrots, squash, oats, sweet potatoes, turnips, berries, grapes, parsnips, beets, apples

Prebiotic Foods

Although all prebiotics are fiber, not all fiber is prebiotic. It has been suggested that prebiotic intake may:

  1. Reduction of risk of intestinal infections
  2. Reduce the prevalence and duration of antibiotic-associated diarrhea
  3. Reduce the inflammation and symptoms associated with inflammatory bowel disease
  4. Exert protective effects to prevent colon cancer
  5. Enhance the bioavailability and uptake of minerals, including calcium, magnesium, and possibly iron
  6. Lower some risk factors for cardiovascular disease
  7. Enhanced Short Chain Fatty Acid (SCFA) production
  8. Improvement and/or stabilization of gut microbiota composition
  9. Improvement of intestinal functions (stool bulking, stool regularity, stool consistency)
  10. Modulation of gastrointestinal peptides production, energy metabolism and satiety and thus promote weight loss and prevent obesity, type 2 diabetes, metabolic syndrome, etc
  11. Initiation (after birth) and regulation/modulation of immune functions
  12. Improvement of intestinal barrier functions (reduce leaky gut occurrence), reduction of metabolic endotoxemia

SCFAs also help regulate sodium and water absorption, and can enhance absorption of calcium and other minerals. In addition, SCFAs act to lower colonic pH, which can inhibit growth of potential pathogens and promote the growth of beneficial bacteria such as bifidobacteria and lactobacilli.

Sources of prebiotics include: Leeks, onions, asparagus, garlic, artichokes, chicory, wheat, oats, and soybeans

Be aware that in certain situations, such as small intestine bacterial overgrowth, prebiotic foods can exacerbate symptoms. This leads in to the concept of the FODMAP diet which has shown to be efficacious in conditions such as irritable bowel syndrome. Read our article on the FODMAP diet, and watch this three minute video which explains how FODMAPs can cause symptoms.

We recommend speaking with a qualified practitioner before starting a FODMAP diet as recent research has raised questions around the long term use of the diet due to it’s potential negative effects on the gut bacteria. There are also theories around including FODMAP foods when treating such conditions as small intestine bacterial overgrowth.

Insoluble Fibre/FODMAPs in I.B.S

Five gastrointestinal endocrine cell types that produce hormones regulating appetite and food intake are abnormal in IBS patients……..Individual dietary guidance for intake of poor FODMAPs and insoluble fibres diet in combination with probiotics intake and regular exercise is to be recommended for IBS patients.

The above quote comes from a review paper published in 2015 discussing diet in IBS. It was discussed how this diet (low FODMAP and insoluble fibre) restored abnormalities in the gastrointestinal endocrine cells (cells in the gut that produce hormones).

An example of the complexity of food reactions is the below quote:

Lactose intolerance depends not only on the expression of lactase but also on the dose of lactose, intestinal flora, gastrointestinal motility, small intestinal bacterial overgrowth and sensitivity of the gastrointestinal tract to the generation of gas and other fermentation products of lactose digestion

Lactose intolerance may be in isolation or as part of a wider intolerance – FODMAPs. So as you can see it may be less about the food per se, certainly with some FODMAP contain foods, and more to do with the environment the food is digested and absorbed in.

Probiotic/Fermented Foods

including natural yoghurt, kefir and sauerkraut. Kefir and sauerkraut can be bought here for those who would prefer not to make their own. Or click on the below links:

  • Home made yoghurt recipe – click here
  • Sauerkraut recipe – click here
  • Kefir:
    • A goats milk kefir can be bought here and a recipe can be found here
    • Coconut kefir can be bought here
    • Kefir grains can be bought here
  • Kombucha can be bought here.

You may also like the kindle book ‘Fermented Foods For a Healthy Gut’ by Alison Jones available on Amazon for £1.99.

Please note certain individuals, for example those with a histamine issue, may experience an exacerbation of symptoms when introducing foods such as sauerkraut. Start with small servings and slowly increase. Speak with a qualified practitioner if you have any concerns or experience a worsening of symptoms.

Vitamin A

This nutrient is essential for the mucosal immune system – the immune system found in the gut which helps regulate our gut bacteria. If preferences allow, eat liver. Liver is a great source of vitamin A. It is thought up to 45% of people have issues converting beta-carotene in to vitamin A and thus for some eating beta-carotene foods may not suffice. Also thyroid function effects the conversion.

Green Pasture Farms offer fresh offal.

Vitamin D

This is an essential nutrient for the immune system. So look to get out in the sun and supplement vitamin D.

Vitamin D works in synergy with vitamin A and vitamin K2.

Omega-3 Fats

Fatty acids (found in oily fish such as salmon, mackerel and sardines) may play a particularly important role in preventing leaky gut. Aim for three portions of oily fish per week.

One of the reasons I like cod liver oil is because it provides all three of the above nutrients – omega 3 fats, vitamin A and vitamin D, among others.


Meat broths, such as a chicken stock, which make excellent bases for soups and gravies are excellent sources of collagen, which is a key protein within the gut lining. Alternatively this product can be supplemented.

Methylation, Choline & Bile

This is something I go in to more detail in, in the webinar I have created on SIBO (available via the shop). Essentially PEMT (phosphatidylethanolamine methyltransferase) is a gene that is important for the formation of the nutrient phosphatidylcholine (PC). Phosphatidylcholine is the most abundant phospholipid. Phospholipids have a number of very important functions. Some of these include:

  • Component of every cell membrane of the human body
  • Antioxidant properties
  • Brain function, including the formation of many important neurotransmitters such as acetylcholine
  • Liver function – Phospholipids are important for maintaining the balance between other lipids such as triglycerides and cholesterol. Phos. Choline also plays an important role in bile acid production.
  • Methylation reactions – More than half of all methylation reactions involve phospholipids
  • Intestinal health – Phosphatidylcholine protects the intestinal mucosal barrier from inflammation.
  • Growth and development – Phospholipids such as choline are critical for growing infants and children

Choline is abundantly found in many whole foods. This includes: egg yolks, sunflower and flax seeds and other nuts and seeds, as well as animal sources such as liver and whole fat dairy products. Another consideration, if it’s determined one has a greater need for phosphatidylcholine, is using whole lecithin.

Remember bile is one of the endogenous protective mechanisms due to its bacteiostatic properties

Methylation is important in choline production!

This podcast (start around 24 minutes in) discusses the liver, methylation, choline and it’s role in SIBO: Click here.


It is no less noteworthy that honey and its constituents appear to have a beneficial influence on intestinal microbiota.


In experimental studies, low dietary magnesium intake (found within deeply coloured green vegetables) alters the microbiota, which in turn is linked to inflammatory cytokine release in the brain and signs of anxiety and depressive behaviour.


In experimental models, various phytochemicals have been shown to protect the intestinal barrier and prevent leaky gut; these include but are not limited to curcumin, green tea catechins, quercetin, resveratrol, cocoa. These have been associated with fatigue reduction, positive mood and lowered risk of depression in humans. Phytochemical’s can also influence the growth of beneficial bacteria, and/or prevent dysbiosis in pre-clinical settings.

Phytochemicals, also referred to as phytonutrients, are found in fruits, vegetables, whole grains, legumes, beans, herbs, spices, nuts, and seeds and are classified according to their chemical structures and functional properties.

Thus ensuring adequate fruit and vegetable intake is important. This can be made more convenient, for some of us, by having a weekly delivery of fresh fruit and vegetables, or/and using gadgets such as the Nutribullet.


Ghee, clarified butter, is a source of butyrate. Butyrate is a short chain fatty acid that is beneficial for the digestive system and has other health benefits. It can be bought in most supermarkets an online.

At the intestinal level, butyrate plays a regulatory role on the transepithelial fluid transport, ameliorates mucosal inflammation and oxidative status, reinforces the epithelial defense barrier, and modulates visceral sensitivity and intestinal motility. In addition, a growing number of studies have stressed the role of butyrate in the prevention and inhibition of colorectal cancer. At the extraintestinal level, butyrate exerts potentially useful effects on many conditions, including hemoglobinopathies, genetic metabolic diseases, hypercholesterolemia, insulin resistance, and ischemic stroke


Zinc is important for gastric acid production. It is also very important in tissue healing and thus maintaining a healthy gut lining (preventing and healing leaky gut). Food sources include oysters, beef, crab, pork and chicken. Other sources include pumpkin seeds, cashew nuts and sea vegetables.


Preclinical studies indicate that physical exercise promotes microbial diversity (which is associated with a healthier state) and increases health-beneficial gut bacteria populations. Moreover, the only study carried out on humans appears to confirm murine model results. The mechanisms proposed for this can be found in this paper here.


Disturbed sleep interferes with gut functions in several ways, and many IBS patients notice an increase in their symptoms when they don’t sleep well.

Fecal Transplant

Fecal transplant is a procedure in which fecal matter, or stool, is collected from a tested donor, mixed with a saline or other solution, strained, and placed in a patient, by colonoscopy, endoscopy, sigmoidoscopy, or enema.

A clinic can be found here. Please note I have no affiliation or experience with this clinic but I know of a couple of people, who have used them and spoke highly go the clinic. I place this here, purely for those who are wanting to research this area further.


Hyper-vigilance and catastrophisation are common findings in those with IBS and CFS. In fact I can quote the World Journal of Gastroenterology:

“The literature suggests that early interdisciplinary diagnostic cooperation between gastroenterologists and body-­‐mind therapists is necessary.”

The appreciation of the significance of the mind in IBS has led to the cognitive–behavioural model of IBS. This model proposes that gastrointestinal symptoms are affected and maintained by interactions between psychological (e.g. emotions, cognitions and behaviour), social (e.g. modelling, support) and physiological factors (e.g. cramps, bloating).

Within this model, the way in which the individual reacts cognitively to recurrent gastrointestinal symptoms (e.g. catastrophising, hyper-vigilance), and life events (e.g. relationship break-­up), will in turn affect emotional responses (e.g. fear, anxiety, depression), the severity of gastrointestinal symptoms and coping ability.

Catastrophising: a term that refers to a bias towards prediction of a high likelihood of worst outcomes. This measure strongly correlates with the severity of pain symptoms and is a primary treatment target in Cognitive Behavioural Therapy.

Hyper-vigilance: the more attention we place on our gut health the more aware of it we are and, potentially, the worse it becomes.

Summary – Restoring Digestive Health In Chronic Fatigue Syndrome

The interventions that are most effective for improving digestive health are very individual and context specific. If you have read all our articles on digestive health then hopefully you understand why.

We cannot underestimate the impact stress, lack of sleep, negative emotions and chronic negative thoughts contribute to poor digestive health.  The most effective way to restoring digestive health in chronic fatigue syndrome is thus a holistic and comprehensive approach that includes supporting the mind, and the body.

This is why we at Conquering Fatigue Successfully focus so much on education. We are all at different stages in our journey, and thus, we all require different strategies and interventions. The greater our level of understanding, the great our level of self-awareness, the more control we have over our future health.