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Make friends with your microbes

* This article was originally produced for the Sheffield ME/CFS Group



References to our microbiota – the term used to describe the 10 – 100 trillion microbial cells we each harbour, are all around, and for good reason.


Our intestines contain approximately 100,000 billion microbes compared to the 1000 billion on our skin and our intestinal microbiota weighs about 1.5kg, which is the same as a liver.


Our microbiome consists of 3.3 million genes compared to human genes of 23,000 which indicate how influential our bugs really are.


Our intestinal tract is our largest barrier with the environment and houses our microbiome but also hosts 80% of our immune system, 60% of our hormones are based in the gut and there are more nerve endings (from our enteric nervous system) than in the skin.


The gut is the foundation of health and has far reaching impacts on your body including:


  • Digestive symptoms: up to 84% of IBS may be the result of dysbiosis – an imbalance in your bacteria;
  • ME/CFS gut bacterial composition is altered, and biomarkers for inflammation and leaky gut are increased;
  • A 2017 study reported that up to 90% of CFS patients also have Irritable Bowel Syndrome and described how the distinct mix of gut bacteria and the metabolic disturbances present in these individuals potentially correlated with the severity of the diseases;
  • Immune dysregulation: Problems like dysbiosis and inflammation (particularly in the gut) can impact immunity.  Functional medicine is clear that ‘leaky gut’ or intestinal permeability is a key driver of autoimmune disease;
  • Brain: Research has shown the link with probiotics (live bacteria) and mood, anxiety and depression.  Not to mention the brain fog that is extremely common in M.E/CFS;
  • Metabolism: Overgrowth of certain strains of bacteria has been linked with being overweight, high blood sugar levels and high cholesterol;
  • Sleep: Inflammation in the intestines is associated with insomnia. Serotonin, our good mood neurotransmitter is primarily made in the gut, and this ultimately is converted into melatonin – our body’s sleep chemical;
  • Skin: Many skin conditions originate in the gut and have been shown to improve with balancing bacterial overgrowth in the gut;
  • Hormones: The bacteria in your gut are crucial in breaking down hormones and removing them from the blood. This is particularly important for women and the removal of Oestrogen. Without a well functioning gut, Oestrogen can re-enter circulation, increasing hormone levels;
  • Inflammatory response: If you have inflammation in your gut it can cause inflammation in the rest of your body, which can lead to fatigue and pain in addition to all the symptoms listed above;
  • Absorbing nutrients: if you cannot absorb the nutrients in your food, it can lead to dry or thinning hair, fatigue, cravings and nutrient deficiencies.



Although M.E/CFS is still of unknown origin, several key factors of health have been implicated as potential drivers of the disease, including gut health. So how can you support your gut and particularly your microbiome?



  • Increase fibre intake.  Fibre is a prebiotic that helps feed beneficial bacteria and supports motility, keeping you regular. Include cruciferous vegetables like broccoli, green leafy vegetables, beetroot, onions, leeks, garlic, sweet potato, avocado, berries, chia seeds, apples etc;
  • Eat a wide variety of plants to increase microbiome diversity.  The more plants you eat, the happier bugs you can feed! These include vegetables, fruits, salads, nuts and seeds and herbs;
  • Avoid sugar and particularly artificial sweeteners and alcohol.  They can lead to overgrowth of unwanted bacteria and may increase sugar cravings, brain fog and weight gain;
  • Try and eat organic where possible. GMO foods contain glycoghosphate, which can damage the gut – resulting in leaky gut and affect the growth of bacteria;
  • Eat Polyphenols. Polyphenols are antioxidants that are fuel for your bugs. Include nuts, seeds, berries, olive oil, brassica’s and green tea;
  • Avoid Gluten. Gluten intake has been shown to result in increased intestinal permeability.  It is also linked with autoimmune disease and contains a similar structure to some body tissues, which can lead to molecular mimicry – this is where your body mistakes your own tissues for gluten and attack’s them;
  • Try bone broth to help support the gut lining and your microbiome;
  • Relax. High levels of stress can negatively alter the composition of your gut bacteria;
  • Implement a sleep hygiene routine. Changes in circadian rhythm are associated with alterations in the gut microbiome;
  • Fermented foods provide lots of beneficial bacteria but introduce them slowly. In some cases, they can exacerbate digestive symptoms.


The health and function of our gastrointestinal system and microbiome is pivotal as they execute numerous activities that are crucial for our health and wellbeing.


What is your gut feeling?





Farre, N. Gozal, D. (2018). ‘Sleep and the microbiome: a two-way relationship’, Archivos de Bronconeumologia (English Edition), 55 (1): 7-8.


Mandarano, A. Giloteaux, L. Keller, B. et al. (2018). ‘Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome’, Peer J, 6: e4282.


Naga-Szakal, D. Williams, B. Mishre, N. et al. (2017). ‘Fecal metagenomic profiles in subgroupd of patients with myalgic encephalomyelitis/chronic fatigue syndrome’, Microbiome, 5:44.


Giloteaux, L. Goodrich, J. Walters, W. et al. (2016). ‘Reduced diversity and altered composition of the gut microbes in individuals with myalgic encephalomyelitis/chronic fatigue syndrome’, Microbiome, 4: 30.


Nagpal, R. Yadav, H. Marotta, F. (2014). ‘Gut microbiota: the next-gen frontier in preventative and therapeutic medicine?’, Frontiers in Medicine, 1: 15.


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