Autoimmune Disease and Diet: What Role Do Gut Health, the Microbiome and Micronutrients Play?

The intestine is one of the body’s major interfaces with the external environment.

Every day it encounters food components, microorganisms and microbial products while maintaining a controlled barrier between the intestinal contents and the rest of the body.

The intestinal immune system therefore performs a difficult balancing act. It needs to tolerate harmless food components and commensal microorganisms while remaining capable of responding to pathogens.

This interaction between the intestine, microorganisms and immune system is often described as the gut-immune axis.

Research increasingly shows that the microbiome, microbial metabolites, intestinal barrier and immune signalling interact closely. Altered microbiome patterns have been described in a range of autoimmune and inflammatory diseases, although the direction of cause and effect is not always clear.

That does not mean all autoimmune disease “starts in the gut”.

It does mean that intestinal biology deserves serious attention.

The gut microbiome describes the microorganisms and their genetic material present in the gastrointestinal tract.

These microorganisms interact with:

• dietary fibre

• bile acids

• intestinal cells

• the immune system

• other microorganisms

They also produce metabolites that can influence biological processes inside and outside the intestine.

One important example is the production of short-chain fatty acids, including butyrate, when certain bacteria ferment dietary fibres.

These metabolites participate in intestinal epithelial function and immune signalling.

Research has identified altered microbiome patterns in several autoimmune and inflammatory diseases. But an important question remains unresolved:

Does an altered microbiome contribute to disease, does the disease alter the microbiome, or do both occur?

The answer is likely to differ between diseases and individuals.

Yes.

Diet is one of the major influences on the intestinal microbial environment.

Different microorganisms use different dietary substrates. A varied diet rich in plant fibres therefore creates a different intestinal environment from a diet dominated by highly refined foods.

Human intervention research has shown that dietary changes can alter microbial activity and immune markers.

In a randomized Cell study, diets rich in fermented foods increased microbiome diversity and were associated with reductions in several inflammatory markers, while a high-fibre intervention altered microbial functional capacity and produced more individualised immune responses. The participants were healthy adults, so this should not be interpreted as evidence that fermented foods treat autoimmune disease.

What it does show is that:

what we eat can influence the microbial and immunological environment of the intestine.

The intestinal barrier is real and biologically important.

It consists of interacting components including:

• the mucus layer

• intestinal epithelial cells

• tight junction proteins

• immune cells

• microbial communities and their metabolites

The barrier is selective rather than completely impermeable. Nutrients need to cross it, while microorganisms and potentially harmful substances must be controlled.

Changes in intestinal permeability have been investigated in gastrointestinal, metabolic and immune-mediated diseases.

The term “leaky gut”, however, is often used much more broadly online than the science supports.

Symptoms such as fatigue, brain fog, bloating or joint pain do not by themselves establish pathological intestinal permeability.

At Centre Algos, we therefore prefer to think in terms of intestinal barrier function, digestive symptoms, disease-specific risks and clinically meaningful investigations, rather than assuming that every chronic condition is caused by “leaky gut”.

There is no single treatment that universally “heals the gut”.

But there are many ways to support intestinal health and address identifiable problems.

Depending on the person, this can include:

• improving dietary quality

• increasing fibre diversity when tolerated

• identifying coeliac disease when clinically indicated

• recognising inflammatory bowel disease or other gastrointestinal pathology

• identifying relevant nutritional deficiencies

• investigating persistent digestive symptoms

• reviewing medications that affect gastrointestinal function

• avoiding unnecessary dietary restriction

• ensuring sufficient protein and energy intake

• including fermented foods where appropriate and tolerated

The objective is not to “detox” the intestine.

It is to create favourable conditions for normal intestinal function and identify problems that require specific attention.

Reducing added sugar is often a sensible part of improving overall dietary quality.

But the reason matters.

It is common to read that “sugar causes inflammation”. Human research is considerably more nuanced than this statement suggests.

Sugar is consumed as part of an overall dietary pattern. Diets containing large quantities of added sugars are often also high in ultra-processed foods and relatively low in fibre, micronutrients and minimally processed foods.

High intake can also contribute to excessive energy intake and poorer metabolic health in susceptible individuals.

The practical objective should therefore usually be:

less added sugar and fewer ultra-processed foods, not a zero-sugar diet.

This particularly means reducing:

• sugar-sweetened drinks

• sweets

• many desserts

• highly sweetened breakfast products

• heavily processed snack foods

It does not mean that fruit needs to be eliminated because it naturally contains sugar.

Whole fruit also provides fibre, vitamins, minerals and numerous bioactive compounds.

A nutritionally rich diet is more useful than trying to achieve “zero sugar”.

Ultra-processed foods are increasingly being studied in relation to metabolic and inflammatory health.

The category includes many industrial products designed to be highly convenient and palatable, often containing combinations of refined starches, added sugars, fats, flavourings, emulsifiers and other additives.

Not every processed food is unhealthy. Frozen vegetables, canned legumes, olive oil and yoghurt are processed to some degree.

The more useful distinction is between nutritious foods that have undergone processing and a dietary pattern dominated by highly refined products with relatively little fibre or micronutrient value.

Reducing the latter creates room for foods that better support nutritional and metabolic health.

Not automatically.

For someone with coeliac disease, strict lifelong avoidance of gluten is an essential medical treatment.

That does not mean gluten causes every autoimmune disease or that everyone with an autoimmune condition should stop eating it.

There may be individual circumstances in which gluten-related symptoms or another diagnosis require investigation. Importantly, removing gluten before appropriate testing can make coeliac disease more difficult to diagnose.

For people without coeliac disease or another clear indication, routine gluten exclusion should not be assumed to improve autoimmune disease.

Some people clearly notice that particular foods worsen gastrointestinal or other symptoms. Those observations deserve attention.

But an individual reaction is different from evidence that an entire food category drives autoimmune disease in everyone.

Blanket elimination of dairy, eggs, legumes, grains, nuts, seeds or nightshade vegetables can make diets unnecessarily restrictive and, if poorly planned, reduce nutritional adequacy.

When food elimination is considered, it should ideally have:

1. a clear clinical reason

2. a defined purpose

3. an appropriate nutritional replacement strategy

4. a plan for reassessment or reintroduction where appropriate

The Autoimmune Protocol, often called the AIP diet, is a highly restrictive elimination diet derived partly from the Paleo diet.

It usually removes multiple food groups before foods are gradually reintroduced.

Small preliminary studies have produced interesting findings in selected conditions, but current evidence is not strong enough to consider AIP an established general treatment for autoimmune disease.

Its restrictive nature also means nutritional adequacy and the psychological burden of eating need to be considered.

For most patients, it should not automatically be the first dietary strategy.

Micronutrients participate in hundreds of biological processes, including immune regulation, energy metabolism, tissue maintenance and blood-cell production.

Autoimmune disease can affect micronutrient status through:

• insufficient dietary intake

• reduced appetite

• restrictive dietary patterns

• altered absorption

• gastrointestinal inflammation

• increased losses

• medication-related effects

• disease-specific nutritional risks

This is why micronutrition is more useful when it is targeted than when it becomes a long list of supplements taken “for immunity”.

Vitamin D

Vitamin D has important functions in bone metabolism and immune biology.

Low vitamin D concentrations are frequently observed in chronic and autoimmune conditions, although association alone does not establish causation.

One particularly interesting trial is VITAL. More than 25,000 adults were followed in a randomized study, and vitamin D supplementation was associated with a 22% lower incidence of confirmed autoimmune disease over approximately five years. This was a prevention trial in older adults, not a treatment trial for established autoimmune disease.

The practical point is straightforward:

vitamin D deficiency is clinically relevant and should be corrected when identified.

Iron and ferritin

Iron deficiency can contribute to:

• fatigue

• reduced exercise tolerance

• weakness

• concentration difficulties

• restless legs

• hair changes

Importantly, iron deficiency can occur before anaemia develops.

This can be particularly relevant when autoimmune or inflammatory disease affects the gastrointestinal tract, when blood loss occurs, or when absorption is impaired.

Ferritin helps assess iron stores, but because inflammation can increase ferritin concentrations, interpretation sometimes requires other markers and clinical context.

Vitamin B12 and folate

Vitamin B12 and folate are important for neurological function, blood formation and cellular metabolism.

Deficiency can occur through inadequate intake, medication effects or impaired gastrointestinal absorption.

Autoimmune gastritis is a particularly relevant example. Progressive gastric atrophy can interfere with both vitamin B12 and iron status.

Coeliac disease and inflammatory bowel disease can create additional nutritional risks.

The useful question is therefore not simply:

“Should I take B12?”

It is:

“Is there a reason I may be deficient, and what does my individual situation show?”

Selenium

Selenium is involved in antioxidant enzymes and thyroid hormone metabolism and is of particular research interest in autoimmune thyroid disease.

Some randomized studies and meta-analyses in Hashimoto’s thyroiditis have reported changes in thyroid-related laboratory markers with selenium supplementation.

That does not mean everyone with Hashimoto’s disease needs selenium.

Requirements are relatively small and excessive intake can be harmful, which is another reason to favour targeted micronutrition rather than indiscriminate supplementation.

Zinc and other micronutrients

Zinc participates in numerous aspects of immune function.

It can be relevant depending on diet, gastrointestinal health and individual nutritional status.

Magnesium and various B vitamins can also deserve attention in particular situations.

At Centre Algos, we do not assume that every person with autoimmune disease requires the same micronutrients.

We look for a clinical reason to investigate or correct them.

Omega-3 fatty acids, particularly EPA and DHA, participate in lipid signalling pathways involved in inflammatory regulation and resolution.

They are found predominantly in oily fish and marine sources, while plant foods provide the precursor alpha-linolenic acid.

Evidence reviews in rheumatic disease suggest some dietary components, including omega-3 in rheumatoid arthritis, can produce modest benefits.

Regularly including appropriate omega-3-rich foods can therefore form part of a high-quality dietary pattern.

Whether supplementation is useful depends on dietary intake and clinical context.

Fermented foods and probiotic supplements should not be treated as the same intervention.

Foods such as yoghurt, kefir, sauerkraut and other traditionally fermented foods can form part of a varied diet when tolerated.

Probiotic supplements contain selected microbial strains at defined doses.

Research into probiotics and immune-mediated diseases is developing, but effects depend on the strain, dose, disease, patient population and outcome being measured.

A benefit from one probiotic strain in one condition cannot be generalised to all probiotics or all autoimmune diseases.

Not necessarily.

Commercial microbiome testing can generate detailed reports describing large numbers of microorganisms.

The technology for identifying microbes has advanced rapidly. The ability to interpret every variation and turn it into an established clinical treatment decision has not advanced at the same speed.

A 2025 international consensus statement concluded that evidence supporting routine clinical use of microbiome testing remains limited and called for stronger standards and clinical validation.

That does not mean stool testing is useless.

It means the test should answer a defined clinical question.

For example, faecal calprotectin is an established stool marker used in appropriate circumstances to help distinguish inflammatory bowel disease from non-inflammatory conditions such as IBS.

At Centre Algos, we can prescribe targeted stool investigations when symptoms, history or other findings provide a clinical reason.

We do not need to turn every patient into a microbiome report.

Broad claim	More useful clinical question
“Leaky gut”	Are there persistent digestive symptoms or gastrointestinal problems that should be investigated?
“My microbiome is bad”	Is there a defined clinical question that a validated investigation can answer?
“I need to eliminate gluten”	Is there evidence or a diagnosis that makes gluten exclusion appropriate?
“I need immune supplements”	Is there a deficiency, absorption problem or specific nutritional need?
“Sugar causes my inflammation”	Would reducing added sugar and improving overall dietary quality improve nutritional and metabolic health?

The relationship works in both directions.

Nutrition can influence health, but autoimmune and inflammatory disease can also alter nutritional status.

For example:

Coeliac disease can damage the small intestinal mucosa and impair nutrient absorption.

Crohn’s disease and ulcerative colitis can affect food intake, intestinal absorption and nutritional requirements.

Autoimmune gastritis can impair iron and vitamin B12 status.

Inflammatory arthritis can affect activity, body composition and cardiovascular risk.

Chronic pain and fatigue can make shopping, cooking and maintaining a balanced diet more difficult.

Medication can add another layer.

This is why nutritional assessment should start with the actual person and diagnosis rather than with a generic autoimmune food list.

Nutrition can be an important component of care.

The most useful model is not:

medicine or nutrition

but:

appropriate medical treatment together with attention to nutrition, metabolic health, digestive function, physical activity, sleep and other relevant factors.

This is the integrative approach we use at Centre Algos.

There is no standard “autoimmune package” that every patient receives.

We begin with the individual.

This includes understanding:

• the diagnosis of an autoimmune or inflammatory disease

• current symptoms

• fatigue and energy

• pain and physical function

• digestive symptoms

• dietary pattern

• food restrictions

• weight or appetite changes

• previous laboratory results

• current medications and supplements

• sleep and recovery

• relevant medical history

• previous treatments

We then determine which questions actually need answering.

Targeted blood investigations

When clinically appropriate, we can prescribe blood investigations that go beyond the standard tests a patient may already have had.

Depending on the clinical question, this can include assessment of:

• iron metabolism

• vitamin B12 and folate-related markers

• vitamin D

• selected micronutrients

• metabolic parameters

• inflammatory markers

• other targeted biological parameters

The purpose is not to search endlessly for abnormal numbers.

It is to identify findings that can help explain symptoms, nutritional risk or treatment priorities.

Digestive and stool investigations

When digestive symptoms, disease history or other findings suggest that the gastrointestinal tract deserves closer assessment, we can consider targeted investigations.

These can include stool testing when there is a defined clinical reason.

The choice of test depends on the question being investigated.

We do not assume that every autoimmune condition is caused by dysbiosis, intestinal permeability or a hidden food intolerance.

Building the treatment plan together

Once we understand the relevant contributors, we discuss the treatment strategy with the patient.

Depending on the individual, this may include:

• dietary changes

• improving food quality

• reducing excessive added sugar and ultra-processed foods

• increasing fibre and plant diversity when appropriate

• correcting identified micronutrient deficiencies

• targeted supplementation

• phytotherapy when appropriate

• digestive support

• sleep and recovery strategies

• physical activity adapted to the person’s condition and capacity

• coordination with existing medical treatment

The plan is individual because autoimmune diseases, and the people living with them, are individual.

For someone with an autoimmune disease who wants to improve their nutrition, a sensible starting point is often much simpler than the internet suggests.

Build meals around minimally processed foods.

Eat a wide variety of vegetables and other plant foods.

Include sufficient protein.

Include healthy fats, particularly olive oil, nuts, seeds and appropriate omega-3 sources.

Increase fibre gradually and according to digestive tolerance.

Reduce foods high in added sugar and refined ingredients.

Limit reliance on ultra-processed snack foods and ready-made products.

Do not remove gluten, dairy or multiple other food groups without a clear reason.

Pay attention to persistent digestive symptoms.

Investigate nutritional deficiencies when the history or disease creates a reason to suspect them.

This approach is less dramatic than a “30-day autoimmune reset”.

It is also much easier to sustain and much closer to what the evidence currently supports.

Not every digestive symptom is caused by diet.

What is the best diet for autoimmune disease?

There is no single diet proven to be best for every autoimmune disease. A high-quality, minimally processed, Mediterranean-style dietary pattern is a strong general foundation, but nutrition should be adapted to the diagnosis, symptoms, nutritional status and individual tolerance.

What foods should I avoid with an autoimmune disease?

There is no universal list. Foods should be excluded when there is a medical indication, such as gluten in coeliac disease, a confirmed allergy or another clear individual reason. Removing multiple food groups without a reason can unnecessarily reduce dietary variety and nutritional adequacy.

Is sugar bad for autoimmune disease?

High consumption of added sugar is best reduced as part of improving overall dietary quality and metabolic health. The evidence does not support treating all sugar as a direct cause of autoimmune inflammation. Whole fruit does not need to be avoided simply because it contains naturally occurring sugars.

Can gut health affect autoimmune disease?

The intestine has extensive interactions with the immune system, and the gut microbiome and intestinal barrier are active areas of autoimmune research. Altered microbiome patterns have been observed in several autoimmune diseases, although cause and effect are not always known.

Does autoimmune disease start in the gut?

Not as a general rule. Autoimmune diseases have complex and disease-specific causes. The gut can contribute to immune regulation and may be particularly relevant in certain diseases, but it should not be presented as the universal origin of autoimmunity.

Can you heal autoimmune disease by healing the gut?

There is no evidence that a general “gut healing” programme cures autoimmune disease. Improving nutrition, treating gastrointestinal disease, correcting deficiencies and supporting intestinal health can nevertheless be valuable parts of an overall treatment strategy.

What is dysbiosis?

Dysbiosis describes an alteration in a microbial ecosystem compared with a reference state. It is a useful research concept, but there is no single universal microbiome pattern that defines dysbiosis in every patient or autoimmune disease.

Should I take probiotics for autoimmune disease?

Not automatically. Probiotic effects are strain-specific and disease-specific, and the evidence varies. A generic probiotic should not be assumed to treat autoimmune disease simply because the microbiome is involved in immune biology.

Should I avoid gluten if I have an autoimmune disease?

Gluten must be strictly avoided in coeliac disease. For other autoimmune diseases, routine gluten exclusion is not automatically necessary. If coeliac disease is suspected, testing should ideally occur before beginning a strict gluten-free diet.

Is the AIP diet scientifically proven?

The Autoimmune Protocol has produced interesting results in small preliminary studies, but current evidence is insufficient to consider it a proven general treatment for autoimmune disease. It is also highly restrictive and should not automatically be the first dietary strategy.

Which vitamins and minerals are important in autoimmune disease?

Vitamin D, B12, folate, iron, selenium and other micronutrients can be relevant depending on the disease, diet, medication and absorption. The useful question is whether an individual has a deficiency or a specific reason for investigation or supplementation.

Is vitamin D important in autoimmune disease?

Vitamin D has roles in immune biology and deficiency should be corrected when identified. A large randomized prevention trial found fewer new autoimmune diagnoses among adults receiving vitamin D, but this does not mean vitamin D alone treats established autoimmune disease.

Can autoimmune disease cause nutrient deficiencies?

Yes. Some autoimmune diseases can affect appetite, dietary intake or gastrointestinal absorption. Coeliac disease, inflammatory bowel disease and autoimmune gastritis are examples where deficiencies can be clinically important.

Are stool tests useful for autoimmune disease?

They can be useful when they answer a defined clinical question, particularly when gastrointestinal symptoms are present. Broad commercial microbiome profiling is different from established targeted stool investigations and is not automatically necessary.

Can Centre Algos test micronutrients and gut health?

Yes. When clinically appropriate, we can prescribe targeted blood investigations and selected stool investigations based on symptoms, history and existing results. The objective is to answer specific clinical questions and use the findings to guide an individual treatment plan.

Autoimmune disease is complex.

There is no single food to blame, no universal microbiome imbalance to correct and no supplement combination that applies to everyone.

But that does not mean nutrition and intestinal health are unimportant.

The gut is closely connected to immune biology. Diet influences the intestinal environment. Autoimmune and inflammatory diseases can alter nutritional status. Micronutrient deficiencies can contribute to fatigue and other symptoms. Dietary quality also influences metabolic and cardiovascular health.

The useful approach is therefore neither to ignore nutrition nor to promise that food can cure autoimmunity.

It is to ask better questions:

Is the diet providing what this person needs?

Are there deficiencies?

Are digestive symptoms telling us something that deserves investigation?

Could absorption be impaired?

Is the diet supporting a healthy gut and metabolic environment?

Are unnecessary restrictions making nutrition worse rather than better?

And most importantly:

Which of these factors can we realistically improve?

At Centre Algos, we combine these questions with the established diagnosis, current symptoms, previous investigations and existing medical treatment to build an individual strategy.

If you live with an autoimmune or chronic inflammatory condition and would like to understand whether nutrition, micronutrient status or digestive health may be relevant to your symptoms, a consultation at Centre Algos allows us to review the wider picture and determine which investigations and treatment strategies are appropriate.

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