As nutritionists and dietitians, we often see patients struggling with complex, persistent conditions like Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), Fibromyalgia (FM), and Long COVID. These disorders are marked by ongoing fatigue, post-exertional malaise, widespread pain, and cognitive difficulties. Despite their growing impact on individuals and healthcare systems worldwide, clear diagnostic tests and definitive treatments are still lacking.
This blog explores the latest scientific findings about the gut’s role in these illnesses and offers practical insights on how diet and gut health can influence symptoms and recovery.1
The Intestinal Barrier: A Key Player in Chronic Illness?
Central to this discussion is the gut-brain axis and the concept of increased intestinal permeability, often called “leaky gut”.2 Research increasingly points to a weakened gut barrier as a possible contributor to systemic inflammation and immune dysfunction seen in FM and ME/CFS.1,2
Patients with FM and ME/CFS often show higher levels of biomarkers indicating gut barrier disruption and bacterial translocation compared to healthy individuals. For example, elevated IgG antibodies to beta-lactoglobulin, a milk protein, suggest food sensitivities linked to gastrointestinal issues. Higher levels of Zonulin-1 (ZO-1) reflect compromised intestinal lining integrity. Increased lipopolysaccharides (LPS), toxins from certain bacteria, and elevated soluble CD14 (sCD14), a receptor involved in immune activation, further highlight ongoing gut-derived inflammation.2,4
Notably, these markers tend to be higher in FM than in ME/CFS, suggesting differences in disease mechanisms. Additionally, many ME/CFS and Long COVID patients show an imbalance in gut bacteria, formerly known as dysbiosis, with fewer beneficial species like Faecalibacterium and Bifidobacterium, and more pro-inflammatory Gram-negative bacteria. This imbalance may drive low-grade inflammation affecting fatigue, pain, and cognition.2,3
Dietary Changes and Targeted Supplements: What Helps?
Given the complex relationship between diet, gut health, and symptoms, lifestyle and nutritional interventions are promising ways to support recovery in CFS and related conditions.1,3
Diets high in processed foods, refined sugars, and saturated fats, and low in fresh fruits and vegetables can worsen nutritional deficiencies and inflammation. Common deficiencies in B vitamins, vitamin C, magnesium, zinc, and essential fatty acids have been linked to fatigue and slower recovery in CFS patients.1
Supplementation targeting mitochondrial function, neuroinflammation, and gut integrity shows potential benefits. Soluble fibers like beta-glucans and inulin serve as prebiotics that nourish gut bacteria, promoting the production of short-chain fatty acids such as butyrate, which has anti-inflammatory and brain-protective effects.5 One clinical trial found that combining beta-glucan with vitamins D3, B6, and zinc improved cognitive fatigue and quality of life, suggesting benefits for “brain fog” symptoms.1,3
Omega-3 fatty acids, often low in these patients, can reduce inflammation and support mood. Supplementing with EPA and DHA supports immunity and eases pain and depression. L-carnitine, essential for mitochondrial energy, is frequently deficient and may reduce fatigue and muscle pain when taken at appropriate doses.1
Restoring levels of key micronutrients like B12, folate, magnesium, zinc, iron, vitamin C, vitamin E, vitamin D, and selenium also supports neurological function, energy metabolism, and immune balance. Mitochondrial cofactors such as CoQ10 and NADH have shown promise in boosting energy and muscle function in ME/CFS.6,7,8.
The Psychobiotic Approach: Healing Beyond the Gut
Probiotics, prebiotics, and synbiotics can help restore gut balance and modulate the gut-brain axis.4. Certain probiotic strains, called psychobiotics, have shown potential for improving mental health by reducing anxiety, depression, and improving sleep and stress resilience.1,3
In ME/CFS and Long COVID patients, probiotic strains like Lactobacillus and Bifidobacterium have been associated with reduced inflammatory markers (e.g., CRP, IL-6) and improvements in fatigue, mood, and cognitive symptoms.3 While results vary and more research is needed, these microbial therapies also often relieve gastrointestinal symptoms such as bloating and diarrhea, especially in patients with coexisting Irritable Bowel Syndrome.1,2,5
Final Thoughts
The gut-brain connection offers a valuable perspective in understanding and managing complex chronic conditions like ME/CFS, FM, and Long COVID. While no single treatment fits all, addressing gut health through diet, targeted supplementation, and microbiome support is a promising, integrative approach worth exploring alongside conventional care.
Implications for Your Practice: A Holistic Horizon in Nutritional Care
For nutritionists and dietitians who are working with individuals who suffer from chronic fatigue and burnout, these findings underscore the importance of a holistic, individualized approach. Are we adequately assessing gut health and micronutrient status in our patients with chronic fatigue and pain conditions?1,3
- Prioritise a nutrient-dense, whole-food diet, emphasising plant-based foods, lean proteins, and healthy fats.
- Consider targeted supplementation based on individual deficiencies and symptom profiles, using evidence-backed dosages and forms.
- Explore the therapeutic potential of prebiotics, probiotics, and synbiotics as adjunct therapies, educating patients on their role in gut-brain axis modulation and immune support.
- Monitor and assess patient outcomes comprehensively, including self-reported symptom questionnaires (e.g., FIS-40, COMPASS-31, PSQI, SF-36, HADS).2,3
The understanding of the gut-immune-brain axis provides exciting new avenues for managing ME/CFS, FM, and Long COVID. By integrating this knowledge into our practice, we can move beyond mere symptom management and work towards truly restoring health and enhancing the quality of life for these patients.1
About the Author
Dr Joanna Michalina Jurek is a director of a science foundation formed as part of a personalized medical centre – Allergen in Poland, and Clinical Nutrition Dietician specializing in immuno-nutrition, nutri-psychiatry, and gut–brain–liver axis research. Previously, she was a postdoctoral researcher at the GEMMAIR Research Group (IISPV, Spain), where she co-leaded international clinical studies on psycho-metabolic disorders in bariatric patients. Joanna’s work focuses on identifying microbiota- and gene-based biomarkers to better understand and support individuals affected by depression, MASLD, metabolic dysfunction, and emotional eating.
With research experience across APC Microbiome Ireland, Vall d’Hebron Institute of Research, and Ulster University, Dr Jurek combines scientific expertise with clinical application. She consults for wellness startups, NGOs, and medical clinics, offering personalized nutrition strategies and supplement protocols for individuals experiencing post-viral fatigue, hormonal imbalances, and burnout.
She is the author of Dietotherapy for Chronic Fatigue Syndrome and Psychodietetics for Everyone, both grounded in evidence-based research and designed to empower patients and practitioners.
References
- Jurek JM. Dietoterapia w Zespole Chronicznego Zmęczenia. Warsaw: Wydawnictwo Naukowe PWN SA; 2021. ISBN: 978-83-01-23676-2.
- Martín F, Blanco-Suárez M, Zambrano P, et al. Increased gut permeability and bacterial translocation are associated with fibromyalgia and myalgic encephalomyelitis/chronic fatigue syndrome: implications for disease-related biomarker discovery. Front Immunol. 2023;14:1253121. doi:10.3389/fimmu.2023.1253121
- Jurek JM, Castro-Marrero J. A narrative review on gut microbiome disturbances and microbial preparations in myalgic encephalomyelitis/chronic fatigue syndrome: implications for long COVID. Nutrients. 2024;16(11):1545. doi:10.3390/nu16111545
- Giloteaux L, Goodrich JK, Walters WA, et al. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome. 2016;4:30. doi:10.1186/s40168-016-0171-4
- Lacasa M, Alegre-Martin J, Sentañes RS, et al. Yeast beta-glucan supplementation with multivitamins attenuates cognitive impairments in individuals with myalgic encephalomyelitis/chronic fatigue syndrome: a randomized, double-blind, placebo-controlled trial. Nutrients. 2023;15(21):4504. doi:10.3390/nu15214504
- Jurek JM, Zablocka-Slowinska K, Pieczynska J, Clavero Mestres H, Auguet T. Systematic review of the effects of plant-based foods on metabolic outcomes in adults with MASLD and comorbidities such as obesity, metabolic syndrome, and type 2 diabetes. Nutrients. 2025;17(18):3020. doi:10.3390/nu17183020. PMID: 41010543; PMCID: PMC12472190
- MyNutriWeb. Nutrition and Inflammation: The role of plant-based diets [webinar]. MyNutriWeb. November 20, 2024. Accessed [today’s date]. https://mynutriweb.com/nutrition-and-inflammation/
- MyNutriWeb. Nutrition and Inflammation Fact Sheet (Inflammation_MNV_factsheet_V7_MC). MyNutriWeb; 2025. Accessed [today’s date]. https://mynutriweb.com/wp-content/uploads/2025/03/Inflammation_MNV_factsheet_V7_MC.pdf
