GUT HEALTH AND AUTOIMMUNE DISEASE: Could a Gut Infection Be Part of the Problem?

If you have an autoimmune disease, you've probably heard that you should "heal your gut."

But what does that actually mean?

And more importantly, what does gut health have to do with autoimmune disease?

This is a question I find particularly interesting in patients who develop autoimmune symptoms after a significant gastrointestinal infection.

Maybe you had food poisoning while travelling.

Maybe you developed persistent digestive symptoms after a bout of gastroenteritis.

Maybe you were diagnosed with H. pylori.

Or perhaps your digestion seemed to change completely before you developed thyroid antibodies, joint pain, inflammatory symptoms, skin problems or another autoimmune condition.

The connection between gut health and autoimmune disease is becoming an increasingly important area of research.

We now understand that the gut microbiome, intestinal barrier and immune system are deeply interconnected. Research has identified differences in gut microbial composition and function across a number of autoimmune diseases, including Hashimoto's thyroiditis, rheumatoid arthritis, systemic lupus erythematosus and multiple sclerosis.

But there is another piece of this conversation that I think deserves more attention:

Gut infections.

Because sometimes the question isn't simply, "How can we improve gut health?"

It is:

"What happened to the gut before the autoimmune disease developed?"

The connection between gut health and autoimmune disease

The gastrointestinal tract is much more than a digestive system.

It is one of the body's largest interfaces with the outside world and contains an enormous concentration of immune tissue.

Every day, the immune system has to decide what belongs in the "tolerate" category and what represents a potential threat.

Food proteins.

Beneficial bacteria.

Pathogenic organisms.

Microbial metabolites.

Environmental antigens.

This requires an incredibly sophisticated balance between immune activation and immune tolerance.

The gut microbiome plays an important role in this process.

Microorganisms living in the digestive tract produce metabolites that interact with intestinal cells and immune cells. Certain microbial metabolites can support regulatory immune pathways, while other microbial signals can promote inflammatory activity.

A 2025 systematic review examining the role of the gut microbiota in autoimmune disease concluded that alterations in microbial communities and intestinal barrier function are increasingly associated with autoimmune pathogenesis, although the precise causal relationships are still being investigated.

A separate 2025 systematic review and meta-analysis found consistent associations between alterations in the gut microbiome, intestinal permeability and several autoimmune diseases, while also finding that some microbiota-directed interventions were associated with improvements in disease activity and immune markers. The authors emphasized that more research is needed before specific microbiome interventions can be considered established treatments for autoimmune disease.

So when we talk about gut health and autoimmune disease, we're not simply talking about digestion.

We're talking about the relationship between:

The microbiome → the intestinal barrier → the immune system.

And gut infections can disrupt all three.

What happens to gut health after an infection?

Think about what happens during a significant gastrointestinal infection.

The immune system becomes highly activated.

The intestinal lining becomes inflamed.

The microbial environment changes.

Sometimes antibiotics are introduced.

Diet changes because you're unable to tolerate your usual foods.

Bowel motility may change.

And the composition of the microbiome can shift.

For some people, everything eventually returns to normal.

For others, the digestive system never quite feels the same again.

The infection may have resolved, but the patient is left with:

• persistent bloating

• reflux

• abdominal pain

• diarrhea or constipation

• new food sensitivities

• fatigue

• changes in bowel habits

• increased inflammatory symptoms

This is one reason I think it is important to distinguish between the infection itself and the aftermath of the infection.

The pathogen may no longer be present, but the intestinal ecosystem and immune environment may have changed.

And in someone who is genetically predisposed to autoimmunity, that altered environment may become one of several factors contributing to loss of immune tolerance.

This is not proof that a previous infection caused an autoimmune disease.

Autoimmunity is multifactorial.

Genetics, hormones, environmental exposures, nutrition, infections, metabolic health and other immune triggers can all contribute.

But the timeline can provide an important clue.

How can a gut infection potentially contribute to autoimmunity?

There are several mechanisms researchers are investigating.

1. Intestinal barrier disruption

The intestinal lining acts as a selective barrier between the contents of the digestive tract and the immune system.

When intestinal barrier function is impaired, microbial products and other antigens may have greater interaction with immune cells.

This can contribute to inflammatory signalling and may be particularly relevant in people who are already genetically susceptible to autoimmune disease.

The concept is often referred to as "leaky gut," but intestinal permeability is the more scientifically appropriate term.

Importantly, increased intestinal permeability is not synonymous with autoimmune disease, and it is not appropriate to assume that everyone with an autoimmune condition has a single "leaky gut" problem that can be fixed with supplements.

The biology is considerably more complicated.

2. Microbiome disruption

A gastrointestinal infection can change the microbial ecosystem.

And the microbiome is part of the immune system's environment.

Research has identified disease-associated changes in microbial diversity, composition and microbial metabolites across several autoimmune diseases.

Some of these changes may be a consequence of autoimmune disease rather than the cause.

This is an important distinction.

The relationship is likely bidirectional:

Gut health can influence immune function, while systemic inflammation and autoimmune disease can also influence gut health.

3. Molecular mimicry

Some infections may also contribute to autoimmunity through a process known as molecular mimicry.

This occurs when components of a microorganism resemble proteins found in human tissue closely enough that an immune response directed against the pathogen may potentially cross-react with the body's own tissues.

Molecular mimicry is one of several mechanisms proposed to explain infection-associated autoimmunity.

This doesn't mean that every infection causes autoimmunity.

It means that, in genetically susceptible individuals, an infection may potentially provide an immune stimulus that contributes to loss of tolerance.

H. pylori and autoimmune disease

One of the most clinically interesting examples is Helicobacter pylori.

H. pylori is a bacterium that colonizes the stomach and can persist for years.

It is best known for its role in gastritis and peptic ulcer disease, but researchers have also investigated its relationship with conditions outside the gastrointestinal tract.

One particularly interesting association is between H. pylori and autoimmune thyroid disease.

A meta-analysis including 15 studies and more than 3,000 participants found that H. pylori infection was associated with autoimmune thyroid disease. The association was also observed specifically with Hashimoto's thyroiditis and Graves' disease.

This is clinically interesting, but it needs to be interpreted carefully.

Association does not prove causation.

The evidence does not mean that H. pylori is the cause of Hashimoto's thyroiditis.

However, if someone has Hashimoto's alongside symptoms such as chronic gastritis, reflux, dyspepsia or unexplained iron deficiency, a history of H. pylori becomes relevant.

Instead of simply asking:

"How do we manage the thyroid?"

it may also be worth asking:

"What is happening in the gastrointestinal tract?"

Gut health, histamine and mast cells

There is another connection that I frequently see clinically: patients with digestive problems who also develop new food reactions, flushing, headaches, itching or other histamine-related symptoms.

The gut contains a large population of mast cells, which are immune cells involved in allergic and inflammatory responses.

Mast cells can release histamine as well as numerous other inflammatory mediators.

And the relationship between the microbiome and mast cells appears to work in both directions.

Research suggests that microbial signals can influence mast-cell activity, while mast-cell mediators can also influence the intestinal environment. A 2025 review described this microbiota–mast-cell interaction as an important component of intestinal immune regulation.

Some intestinal bacteria can also produce histamine.

Certain bacterial species contain enzymes that convert histidine into histamine, creating another potential link between changes in the gut microbiome and histamine-related symptoms.

But this is where nuance matters.

Finding a bacterium that can produce histamine does not automatically mean that the organism is responsible for someone's symptoms.

Histamine production depends on the specific organism, its abundance, the intestinal environment and the individual's ability to metabolize histamine.

And having food reactions does not automatically mean someone has mast cell activation syndrome (MCAS).

MCAS is a specific clinical diagnosis and should not become a catch-all explanation for unexplained digestive symptoms.

The broader point is simply that:

The microbiome, intestinal immune system and mast cells communicate with one another.

When the gut environment changes, those interactions can change too.

Could a gut infection be the first domino?

Consider a patient who was completely healthy until a significant gastrointestinal infection.

The infection resolves.

But afterward:

She develops chronic bloating.

Then reflux.

Then new food sensitivities.

Then fatigue.

Eventually, thyroid antibodies become positive.

Is it possible that the original infection contributed to the autoimmune disease?

Potentially.

Can we prove that it caused it?

Usually not.

There may have been genetic susceptibility that existed long before the infection.

There may have been other environmental or hormonal triggers.

The infection may have been one of several "hits" that shifted the immune system away from tolerance.

This is how I think about the relationship between gut health and autoimmune disease.

Not as one simple cause and effect.

But as a complex interaction between genetics, the immune system, the microbiome and environmental triggers.

What should you investigate if you have autoimmune disease and digestive symptoms?

This is where personalized assessment becomes important.

I don't believe every patient with an autoimmune disease needs extensive infectious or microbiome testing.

The right question is:

What does the patient's history tell us to investigate?

Some of the questions I would consider include:

Was there a significant gastrointestinal infection before symptoms began?

Food poisoning, travel-related illness, prolonged gastroenteritis or another documented infection can provide an important timeline.

Did digestion change after the infection?

Persistent bloating, reflux, diarrhea, constipation or abdominal pain may suggest that the gut did not fully recover.

Is H. pylori a possibility?

This becomes particularly relevant with upper-GI symptoms, gastritis, dyspepsia or unexplained iron deficiency.

Is there evidence of ongoing intestinal inflammation?

This should be evaluated appropriately rather than assuming that all digestive symptoms are simply "dysbiosis."

Could medications or antibiotics have altered the gut microbiome?

Antibiotic exposure can substantially influence microbial communities, and the effects can persist beyond the period of treatment.

Are there symptoms suggestive of mast-cell or histamine involvement?

Flushing, itching, hives, episodic GI symptoms and reactions involving multiple organ systems may warrant further investigation.

The goal isn't to test everything.

The goal is to identify the most clinically relevant pieces of the puzzle.

How do you improve gut health when you have an autoimmune disease?

This is where I think the conversation often becomes too simplistic.

There is no universal "autoimmune diet."

There is no single probiotic that fixes the microbiome.

And taking a long list of supplements isn't the same thing as improving gut health.

A more useful approach is to identify what is actually disrupting the gastrointestinal environment.

That may mean addressing:

An active infection

Post-infectious digestive dysfunction

Inflammation

Nutritional deficiencies

Altered bowel motility

Poor dietary diversity

Low fibre intake

Excessive alcohol intake

Sleep disruption

Metabolic dysfunction

or other individualized factors.

If an infection is present, it should be appropriately treated.

If the gut has been disrupted following an infection, the next step is understanding what has changed rather than simply throwing probiotics at the problem.

And if someone has an established autoimmune disease, gut-focused care should complement — not replace — appropriate conventional medical treatment.

The gut may be part of the autoimmune story

The relationship between gut health and autoimmune disease is complex.

We cannot say that poor gut health causes every autoimmune disease.

We cannot say that treating the gut will cure autoimmunity.

And we cannot assume that every patient with digestive symptoms has dysbiosis, intestinal permeability or MCAS.

But we also shouldn't ignore the gut.

The microbiome interacts with the immune system.

The intestinal barrier regulates exposure to microbial and dietary antigens.

Gut infections can profoundly alter the intestinal environment.

And emerging research continues to identify associations between gut microbial changes and autoimmune disease.

For some patients, the most important clue may be found in the timeline.

What happened before the autoimmune disease appeared?

Was there an infection?

Did digestion change?

Did food tolerance change?

Did inflammation begin?

Did the immune system start behaving differently?

Sometimes the diagnosis is simply the point at which the problem became measurable.

The biological story may have started much earlier.

And for some people, that story may begin in the gut.

Frequently Asked Questions

Can poor gut health cause autoimmune disease?

There is increasing evidence linking the gut microbiome, intestinal barrier function and immune regulation with autoimmune disease. However, autoimmune diseases are multifactorial, and there is not enough evidence to say that poor gut health alone causes autoimmune disease.

Can a gut infection trigger autoimmune disease?

Certain infections can act as immune triggers in genetically susceptible individuals. Researchers have proposed mechanisms including molecular mimicry, altered immune signalling and disruption of the intestinal environment. However, an infection should be considered one potential contributing factor rather than a universal cause of autoimmune disease.

Is H. pylori associated with Hashimoto's?

Research has found an association between H. pylori infection and autoimmune thyroid diseases, including Hashimoto's thyroiditis. A meta-analysis of 15 studies found an association between H. pylori infection and autoimmune thyroid disease, although this does not establish that H. pylori causes Hashimoto's.

Can gut bacteria produce histamine?

Yes. Certain bacterial strains can produce histamine through histidine decarboxylase activity. However, the presence of a potentially histamine-producing organism does not by itself establish that it is causing histamine-related symptoms.

Is gut health important if I have Hashimoto's?

Gut health may be relevant because the gastrointestinal microbiome and immune system interact closely, and research has identified differences in the gut microbiome of people with autoimmune thyroid disease. However, gut-focused care should be individualized and should complement appropriate medical management of Hashimoto's.

References

1. Adawi M. The role of gut microbiota in autoimmune disease progression and therapy: a comprehensive synthesis. Front Microbiomes. 2025.

2. Vineesh A, et al. Exploring the Relationship Between Gut Health and Autoimmune Diseases: A Systematic Review and Meta-Analysis. Cureus. 2025.

3. Hou Y, et al. Meta-analysis of the correlation between Helicobacter pylori infection and autoimmune thyroid diseases. Oncotarget. 2017.