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PART 3: Optimising Gut Microbiome Health in Long COVID: Time for a new approach

In my previous instalments, I presented the complexities of the gut microbiome in Long COVID and explored the hypothesised and confirmed scientific mechanisms underpinning this multifaceted relationship. Now, I want to turn your attention to practical interventions that can effectively support gut microbiome health and overall well-being.

The interconnectedness of the gut, immune system, and nervous system cannot be overstated. In my clinical practice, over the last 4 years, I've observed that addressing the state of hyperactivation often described by clients is a crucial starting point. This "switched on" state, as many patients describe it, likely stems from the mechanisms I’ve previously discussed, however there is much more to this puzzle.

Before embarking on any health protocol, it's essential for me to assess the following fundamental aspects:

  • Circadian rhythm alignment

  • Outdoor exposure

  • Hydration status

  • Environmental cleanliness

  • Basic physiological functions (sweating, salivation, urination, and bowel movements)

I believe that Long COVID researchers may be overlooking critical elements in optimising health outcomes. Our evolution is intrinsically linked to nature, yet modern lifestyles often contradict natural laws. We've gradually shifted away from outdoor living, developed a fear of sun exposure, rely heavily on sunscreens and sunglasses, consume non-local and chemically treated foods, face chronic exposure to artificial light at inappropriate times, and struggle with addiction to mobile devices, social media, and stress.

This begs the question: How can one truly heal while living in such stark contradiction to our natural state?

While standard interventions in my clinical practice lead to significant improvements in patient outcomes, my research has led me to prioritise circadian rhythm balancing as a foundational step in treatment protocols.

Why is this so crucial?

The answer lies in the profound impact of circadian rhythms on our biological functions, including the health of the gut microbiome. By aligning our daily routines with nature's 24-hour cycle, we will create an optimal environment for healing and restoration.

How do we achieve this?

The process involves restructuring daily and nightly routines to align with natural rhythms. This includes modulating light exposure, optimising meal timing, and implementing sleep/wake cycle training. It's important to note that these rhythms vary based on geographical latitude and genetics.

Valuable insights about gut microbiome health have emerged from studying the Hadza, a group of traditional hunter-gatherers in Tanzania. Their microbiomes exhibit a cyclic succession of species that correlates with seasonal changes, potentially linked to both food availability and seasonal light variations. This raises an intriguing question: Could the year-round abundance of food and indoor living in northern latitude Western societies be detrimental to our microbiome health?

Emerging research has uncovered another critical factor: the gut microbiome's responsiveness to both natural and artificial light spectra. Recent studies have demonstrated:

  • Chronic blue light exposure from LED sources can induce gut dysbiosis related to cholesterol dysregulation.

  • Constant light exposure alters gut microbiota and promotes steatohepatitis progression in high-fat diet rats.

  • The field of "Photobiomics*" is exploring how various forms of light, including photobiomodulation, can influence the microbiome. *Photobiomics is a scientific field that explores the interactions between light and the microbiome.

In light of these findings, my clinical approach incorporates comprehensive circadian rhythm retraining. This involves optimising light and dark cycles, prescribing specific outdoor exposure times, addressing meal timing, light hygiene, moderating technology use, and applying targeted nutritional interventions to support the gut microbiome. The results have been nothing short of remarkable.

Clinical roadmap

Building upon these foundational interventions, I present a comprehensive clinical roadmap for addressing Long COVID. It's crucial to note that this approach is tailored to each individual, taking into account their unique sensitivities, functional capacity, and current medication regimen.

Comprehensive Blood Work Analysis via GP:

In addition to standard blood panels to help tailor specific interventions. I emphasise the importance of a clotting profile, alongside viral, immunoglobulin, lipid, hormone screen, nutritional and pathogen markers. These tests often reveal invaluable insights, negating the need for costly functional testing. Frequently, results indicate some degree of immune deficiency, particularly in IgG subclasses, active latent pathogens, elevated cholesterol, low globulins, and disruptions in B12, folate, iron, and vitamin D metabolism.

In-depth Case History and Nutritional Assessment: 

A thorough nutritional evaluation is paramount for Long COVID patients due to the heightened risk of nutrient deficiencies. The condition can significantly impair nutrient absorption and metabolism, potentially leading to deficiencies in essential vitamins, minerals, proteins, and other crucial compounds.

Gastrointestinal disturbances in Long COVID mean that many patients use medications such as Proton Pump Inhibitors and H2 blockers like Famotidine. While these medications reduce stomach acid production, to help suppress symptoms, they simultaneously suppress vital digestive secretions necessary for optimal nutrient absorption and overall digestive function.

Moreover, Long COVID frequently presents with gastrointestinal symptoms, gut microbiome imbalances, and light sensitivity that limits sun exposure, further compromising nutrient status. Coupled with the debilitating fatigue experienced by many patients, which often impedes meal preparation, a comprehensive nutritional assessment becomes indispensable for tailoring appropriate dietary and lifestyle recommendations.

Hydration Optimisation: 

I've observed remarkable clinical outcomes by addressing hydration levels. While traditional electrolyte replacement formulas can be beneficial, I find many commercial options contain subpar formulations laden with unnecessary ingredients and artificial sweeteners.

Proper hydration is fundamental for enhancing energy levels, increasing blood volume, facilitating cellular communication, and bolstering detoxification processes. Optimal hydration and electrolyte balance facilitate nutrient exchange and support the production of stomach acid and bile salts, crucial for optimised digestion. It's important to note that some individuals may be sensitive to electrolyte replacement, requiring careful and gradual introduction. In many cases well-filtered or natural spring water is often just enough.

Cleaner electrolyte brands:

  • Elete: A high-quality electrolyte replacement containing balanced levels of sodium, potassium, and magnesium, free from artificial sweeteners or potential reactive additives

  • E-Lyte by BodyBio: Similar composition to Elete

  • ConcenTrace by Time Health: A low-sodium electrolyte option, particularly beneficial for those already on sodium supplementation as per cardiologist recommendations

Advanced Hydration Strategies (Under practitioner guidance only):

  • Deuterium-depleted water

  • Hydrogen-enriched water

Addressing Lipid Balance:

The interplay between omega-3 and omega-6 fatty acids is far more nuanced than you see on social media platforms. The widespread notion that omega-3s are universally beneficial while omega-6s are harmful has led to over-supplementation of omega-3 fatty acids, particularly among those with chronic illnesses.

In reality, both omega-3 and omega-6 pathways are crucial for regulating inflammation and maintaining bodily homeostasis. These pathways are interconnected, with the enzyme delta-6-desaturase playing a pivotal role in converting parent fatty acids (alpha-linolenic acid and linoleic acid) into their more biologically active forms.

Impairment of delta-6-desaturase activity, whether due to genetic factors, nutritional deficiencies, lack of outdoor exposure, or inflammation, can result in a relative deficiency of essential omega-6 metabolites, such as arachidonic acid (AA).  Please note that I am not promoting the use of industry produced plant oils that are highly unstable and likely toxic to humans.

Whilst EPA and DHA supplementation can be beneficial in certain contexts, I often find that DHA is more clinically deficient in my clients, with EPA frequently observed in excess. Indiscriminate high-dose EPA and DHA supplementation can disrupt the delicate balance between omega-3 metabolites, potentially leading to unintended consequences such as impaired inflammation resolution, altered immune function, or disrupted tissue repair processes. Regular testing in my clinic consistently reveals insufficiencies in delta-6-desaturase activity, elevated EPA, and low levels of AA, GLA, and DHA.

My preferred interventions include:

  • Prioritising dietary adjustments – encouraging consumption of foods rich in these essential components, primarily fish, and other seafood, as well as grass-fed fatty meats, eggs, butter, ghee and coconut oil.

  • For those who cannot tolerate these foods, or do not eat them for ethical or religious reasons, need to apply specific interventions to optimise lipid balance.

  • In select cases, I may recommend supplemental fats, but these are specialised interventions not suitable for indiscriminate use.

Stabilising Toxic Metabolites in the Gut:

As previously discussed, the dysregulation of the gut ecosystem in Long COVID can lead to accelerated production of toxic metabolites, outpacing the body's ability to metabolise them. For a deeper understanding, I recommend going back over Dr Carlo Brogna's work on this subject and reading my previous blog posts.

In this context, binders can serve as a helpful supportive measure while working to restore gut microbiome balance. These compounds act as 'sponges' or 'attractors' of toxic metabolites. One binder I frequently use is Toxaprevent, which has been proven to remain within the gut without systemic absorption. It has shown efficacy in reducing histamine intolerance symptoms and appears to alleviate certain Long COVID symptoms over a four-week regimen. 

However, I caution using binders too. Some forms can interfere with medication absorption, alter the half-lives of medication and bind to essential nutrients, careful timing of administration, is required. It is also important to note that many commercial binders do not disclose their particle size – this is a crucial factor, as binders like zeolite, humic acids, and charcoal should not enter systemic circulation. Binders must be avoided in individuals with complex medication regimens or who experience chronic constipation.

For many clients, I prefer natural binding methods, primarily through specific fibres, pectins and increased dietary fats.

Antimicrobial Administration:

It is imperative NOT to use antimicrobials without guidance from a knowledgeable practitioner.

Rethinking "Gut Healing"

As my understanding deepens through expert insights and client experiences, I've come to realise that our approach to gut health may be fundamentally flawed. The notion that we can simply supplement our way to optimal gut health contradicts nature's intricate design. While the medicalisation of microbiome research has brought much-needed attention to this field, and some great things are happening in this space, I have significant reservations about its current trajectory and the potentially misleading information reaching the public.

Probiotics: Navigating a Complex Landscape

The probiotic market is a mixed bag of truly innovative products and subpar offerings, accompanied by a deluge of misinformation. As I delve deeper into this space, my scepticism grows. So here are some helpful tips to help you navigate this complex landscape:

  • Look for probiotics backed by clinical data demonstrating efficacy for specific conditions, they generally carry a higher price tag.

  • Seek products that clearly list both bacterial species and strains.

  • Be wary of products that don't specify bacterial strains - these are often generic, potentially imported from China, and lack meaningful supporting data.

Here is an example of a clearly labelled probiotic supplement, you can see clearly the bacteria species and strain/number and you can see that each strain has been registered and trademarked making it easier to trace the source.


This is an example of a label which only provides the name of the bacteria and no other information, it is not clear what strains are being used and where these strains have been sourced.  I would personally disregard this probiotic based on this label.


When considering probiotic supplementation, it's crucial to consider Carlos Brogna's work on potential bacteriophage activity with certain viruses. Some bacterial strains could potentially serve as replication sites for viral of spike persistence.

Given these complexities, I hesitate to provide blanket recommendations for probiotic supplementation. By focusing on other gut health interventions, the microbiome often recovers well without probiotic supplements.

Postbiotics: The Butyrate Focus

Postbiotics, particularly butyrate, show promise in managing Long COVID symptoms, especially in stabilising mast cell activation. Butyrate, naturally produced through dietary fibre fermentation, supports gut health, reduces inflammation, and modulates the immune system - all critical for Long COVID patients.

While research links plant-based and Mediterranean diets to increased butyrate production, there's insufficient comparative research between healthy animal-based and plant-based diets. This knowledge gap makes it challenging to definitively recommend the most effective gut-supporting diet. Ultimately, finding what works best for your individual symptoms is a much better approach than adhering to any specific nutritional dogma.

Prebiotics and Gut Health

The role of dietary prebiotics in supporting butyrate production is thought to be well-established in nutrition science. However, interpreting current nutritional research can be challenging. Studies often lump whole animal-based foods with processed meats, and major research is frequently funded by food industry giants, potentially skewing nutritional narratives. The difficulty in conducting truly unbiased, comparative clinical studies on nutritional interventions often leaves clinicians reliant on government guidance.

Interestingly, many individuals with food sensitivities or chronic illnesses thrive on ketogenic or low-carbohydrate diets – which is a stark contrast to mainstream dietary advice and the popular low fat, low meat, high carb, high plant oil, dietary interventions that are continuously repeated in scientific papers.

How to heal the gut

While microbiome research has seen some remarkable breakthroughs, such as faecal microbiome transplants for treating Clostridium difficile infections, the efficacy of probiotics and other targeted microbiome interventions must be considered within their specific, proven contexts.

The gut's remarkable self-healing abilities often go underappreciated. By optimising health via environment, nutrition, circadian rhythm alignment, and mindful practices, you can significantly enhance gut health without heavy reliance on supplements.

Lessons from the Hadza: Reconnecting with Natural Rhythms

I believe that we are overlooking a fundamental aspect of gut health by not appreciating the lessons from communities like the Hadza tribe. Their lifestyle offers valuable insights:

  • Reduced dependence on pharmaceuticals and supplements

  • Consumption of food that is sources from their natural environment.

  • Avoidance of pesticides and glyphosate-treated foods

  • Alignment with natural daily and seasonal cycles

  • Living in a close tight knit community

The challenge of adopting these approaches in westernise societies often reflects how disconnected we've become from natural living. When conventional medications and supplements lose their effectiveness, which they are and will continue to do so, it may be time to reconsider our approach and return to more fundamental lifestyle changes.

Final Thoughts

I want to say a big thank you to everyone who has read, listened to and supported my posts.  Without your likes, comments and shares my information goes nowhere, if you find value in this content, I encourage you to consider subscribing to my website to stay abreast of future updates. Furthermore, I greatly appreciate when readers share this information across their social media networks, to help spread my message.


Learn with me

I am excited to announce the first of my series of masterclasses to help educate clinicians and support those experience chronic health conditions. If you want to learn more about my interventions, then please do consider my early bird offer on my latest masterclass series that will be released on the 1st August 2024.  The subject this time is A new approach to managing histamine intolerance and mast cell activation syndrome and more details can be found here:

Early Bird: £45.00

After 15th July 2024: £75.00



The information provided in this blog post is for educational and informational purposes only. It is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a medical condition or treatment, and never disregard professional medical advice or delay in seeking it because of something you have read in this post.
This content does not establish a consultant-patient relationship. The author is not responsible for any adverse effects or consequences resulting from the use of any suggestions, preparations, or procedures described in this post. Individual results may vary, and what works for one person may not be suitable for another.
The dietary and lifestyle changes, supplements, and treatments discussed in this post may interact with medications or have contraindications for certain individuals. Do not start, stop, or change any treatment regimens without first consulting your healthcare provider.
If you think you may have a medical emergency, call your doctor or emergency services immediately. Reliance on any information provided in this post is solely at your own risk.



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