If you live with an autoimmune condition, you already know the pattern: good weeks, then a flare that seems to come from nowhere. Fatigue, sore joints, gut upset, brain fog. Different diagnoses, but the same underlying cause: chronic inflammation, often rooted in the gut microbiome. Research has found gut dysbiosis, an imbalance in your gut bacteria, is a common link across most autoimmune conditions studied. It weakens the gut lining, making it more permeable or “leaky” and letting bacterial fragments into your bloodstream that keep your immune system on constant alert.

I know this from personal experience. I was diagnosed with an inflammatory bowel disease in my 20s and spent decades managing symptoms when medication alone wasn’t enough. What finally changed things was functional testing. Microbiome stool testing and SIBO breath testing showed me that dysbiosis was actually driving my inflammation.

Finally, I could treat it, rather than guess.

Here’s what I’ve learned, clinically and personally: in autoimmune disease, the gut microbiome is often where inflammation starts — and where we have the most leverage to improve it.

First, not all inflammation is bad

Inflammation is your immune system’s way of protecting you. Cut your finger, catch a virus or get stung by a bee, and your body sends in a rapid-response team to contain the damage and start repairs.

Acute inflammation is short and protective. You’ll notice redness, heat, swelling, pain or loss of function, and it resolves within days to a couple of weeks. The outcome is healing.

Chronic inflammation is low-grade and never fully switches off. It’s often subtle: fatigue, aches, gut symptoms, brain fog, recurring flares that can persist for months or years, causing ongoing damage to cells, tissues and organs.

Over time, chronic inflammation stops being a response to disease and becomes part of what drives it.

What keeps chronic inflammation switched on?

In autoimmune disease, the immune system mistakenly targets the body’s own healthy tissue — the thyroid in Hashimoto’s, the joints in rheumatoid arthritis, the gut lining in Crohn’s and ulcerative colitis. Each condition looks different, but chronic inflammation is the common driver of symptom severity. Common contributors include:

• An unresolved trigger — an infection or injury that never fully settled
• Gut dysbiosis and increased intestinal permeability (“leaky gut”) — more on this below
• A diet heavy in ultra-processed food, added sugar and refined flour, and low in fibre and plants
• Ongoing stress and poor sleep, which shift the immune system into an overactive state
• Movement extremes — inactivity promotes inflammatory visceral fat, while chronic over-training can add to the load
• Environmental exposures — pollution, chemicals, smoking

Whether it’s the cause or the consequence, bringing down inflammation is central to managing chronic illness.

The gut microbiome and autoimmune disease: where it often starts

If there’s one place to look when you want to reduce inflammation in autoimmune disease, it’s your gut. Most of your immune tissue sits just beneath your gut lining, separated from trillions of microbes by a barrier only one cell thick.

That proximity is deliberate. From birth, your gut microbes train your immune system to tell friend from foe — what to tolerate (food, beneficial bacteria, your own tissues) and what to attack (genuine pathogens). Autoimmunity is, at its core, a breakdown in that tolerance.

Genes load the gun, but they don’t fully explain who develops autoimmune disease. In animal studies, mice that are genetically prone to arthritis stay healthy when raised germ free and develop joint inflammation once specific gut bacteria are introduced. Your microbiome is one of the most important environmental triggers, and unlike your genes, it’s something you can change.

4 ways an imbalanced microbiome fuels autoimmunity

1. A leaky gut barrier. Dysbiosis weakens the tight junctions between gut lining cells. Bacterial fragments such as lipopolysaccharide (LPS) and partially digested food proteins then slip into circulation, keeping the immune system on constant high alert.

2. Losing your anti-inflammatory bacteria. Beneficial species ferment fibre into short-chain fatty acids, especially butyrate. Butyrate feeds your gut lining and supports regulatory T cells (Tregs) — the immune system’s peacekeepers. Lose those bacteria and the balance tips toward inflammatory Th17 cells, which drive tissue damage in many autoimmune conditions.

3. Mistaken identity. Some bacterial proteins closely resemble human ones. When the immune system mounts a response against a microbe, it can cross-react with similar-looking proteins in your own tissues — a process called molecular mimicry.

4. Bacteria in the wrong place. In a 2018 study published in Science, a gut bacterium called Enterococcus gallinarum crossed a damaged gut barrier into the liver and lymph nodes of autoimmune-prone mice and triggered autoantibodies. Researchers then found the same microbe in liver biopsies from people with lupus and autoimmune liver disease.

What a microbiome test can show you

This is why I don’t start with a generic anti-inflammatory list. Two people with the same diagnosis can have completely different gut drivers. A comprehensive stool test can show:

• Diversity — how resilient your gut ecosystem is
• Your butyrate producers — whether species like Faecalibacteria prausnitzii and Roseburia are present in healthy numbers
• Inflammatory and opportunistic species — overgrowths linked with immune activation
• Gut barrier and inflammation markers — such as zonulin, calprotectin and secretory IgA, depending on the test
• Fungal and parasitic overgrowth

Where the Autoimmune Protocol (AIP) fits

The Autoimmune Protocol is an elimination-and-reintroduction diet. It temporarily removes foods that commonly aggravate the immune system or gut: grains, gluten, dairy, eggs, legumes, nightshades, nuts, seeds, refined sugar, alcohol and processed foods while doubling down on nutrient-dense vegetables, quality protein and healthy fats. Foods are then reintroduced one at a time to see what you actually tolerate.

The research is still small, but encouraging:

• IBD: In a pilot study of 15 people with active Crohn’s or ulcerative colitis, 73% reached clinical remission by week 6, and all maintained it through the maintenance phase. Quality-of-life scores also improved.
• Hashimoto’s: A 10 weeks study in 17 women found significant improvements in quality of life and symptom burden, with signs of reduced systemic inflammation (measured by CRP). Thyroid antibodies didn’t shift in that timeframe, but I have seen them shift over time.

AIP is a short-term tool, not a forever diet and the reintroduction phase is key. Staying restricted long-term can narrow your microbiome and risk nutrient gaps. Microbiome testing alongside can show whether your priority is restoring fibre-loving bacteria, addressing overgrowth or repairing the gut barrier.

6 gut-first ways to reduce inflammation in autoimmune disease

1. Feed your anti-inflammatory gut bacteria

This is the foundation everything else builds on. Your butyrate-producing bacteria need fermentable fibre to thrive, and in return they calm your immune system and strengthen your gut barrier.

• Prebiotic fibres: cooked-then-cooled potato or rice, green banana, oats, ground flaxseed, leeks, onions and asparagus (if tolerated)
• Polyphenols: berries, extra virgin olive oil, green tea, cacao and pomegranate help feed beneficial species such as Akkermansia
• Fermented foods: sauerkraut, kimchi, kefir or coconut yoghurt — start with a teaspoon and build up
• Go slowly: if fibre makes you bloat, that’s a clue, not a failure. It can point to SIBO or slow motility, and it’s worth testing before you push through.

A note on probiotics: benefits are strain-specific, and a generic supermarket product may do little for your gut. Your test results show which bacteria actually need support.

2. Eat the rainbow — your microbes love variety

Colourful plants are packed with phytonutrients: the compounds that give food its colour, flavour and aroma, and act as antioxidants that help quieten inflammation. Variety matters as much as volume — different plant fibres feed different gut bacteria. Aim for 30 different plants a week, counting vegetables, fruit, herbs and spices, and lean on dark leafy greens.

3. Cook with anti-inflammatory spices

Turmeric, ginger, garlic, cinnamon and cloves all have antioxidant and anti-inflammatory properties — and they count toward your plant total.

4. Check your vitamin D

Vitamin D helps regulate immune function, and low levels are common in people with autoimmune conditions. Unless you send enough time outdoors without sunscreen in the mornings before the heat of the day, supplementation may be the better option. Food sources include salmon, sardines and eggs.

5. Protect your sleep

Sleep is when your body repairs and recalibrates its immune response — even one bad night raises inflammatory markers. Aim for 7–9 hours with a consistent bed and wake time. Switch off screens an hour before bed, keep the room cool and dark, and use whatever helps you wind down: breathwork, a bath, music, a book.

6. Lower your stress load

Chronic stress keeps cortisol and inflammatory signalling elevated and directly affects your gut via the gut–brain axis. Mindfulness meditation, yoga and tai chi have all been shown to improve stress resilience, and research suggests mindfulness practices may reduce inflammation in chronic inflammatory disease. Start with five minutes a day.

Bonus: move most days. Regular moderate movement such as walking, swimming or strength work lowers inflammatory markers. Match intensity to your energy — in a flare, gentle beats intense.

Test, don’t guess

Symptoms tell you something is wrong. They don’t always tell you why.

I combine microbiome testing, SIBO breath testing (when indicated) and a review of your pathology with a detailed health history. That shows me what’s driving your inflammation, so your food, supplement and lifestyle plan is built around you.

Struggling with autoimmune or gut symptoms? Book a discovery call here.

If you’re ready to understand your gut health a little better, follow along on Instagram. 💚

In clinic, I often see women who are on thyroid medication, whose blood tests look “normal”, and who still feel tired, bloated, foggy and constipated. Medication replaces the hormone. It doesn’t address why the immune system is attacking the thyroid in the first place, and that is where the gut comes in.

How does the thyroid work?

Your thyroid is a small, butterfly-shaped gland at the front of your neck, just below your Adam’s apple. Its hormones help regulate almost every system in your body, including metabolism, energy, body temperature, heart rate, digestion, mood, brain function and bone health.

The thyroid uses iodine and the amino acid tyrosine from your diet to make two main hormones:

• T4 (thyroxine): about 80% of what the thyroid releases. T4 is a storage form that needs to be converted into T3 before your cells can use it.
• T3 (triiodothyronine): the active hormone. The thyroid makes a small amount directly, and most of your T3 is made from T4 in tissues like the liver, kidneys and gut.

Your brain controls how much hormone the thyroid makes. The hypothalamus releases thyrotropin-releasing hormone (TRH), which tells the pituitary gland to release thyroid stimulating hormone (TSH). TSH then tells the thyroid to produce more T4 and T3. This feedback loop is called the hypothalamic-pituitary-thyroid (HPT) axis.

This system can be thrown off by nutrient deficiencies, chronic stress, infections, environmental toxins, inflammation, gut dysbiosis and autoimmunity.

Hashimoto’s and Graves’ disease

There are two main types of autoimmune thyroid disease.

Hashimoto’s thyroiditis is the most common. The immune system attacks the thyroid, causing inflammation and gradual damage to thyroid cells, so over time the thyroid makes less hormone (hypothyroidism). Symptoms can include fatigue, weight gain, constipation, feeling cold, dry skin, thinning hair, joint and muscle aches, low mood and heavy periods. It is far more common in women.

Graves’ disease happens when antibodies switch the thyroid on, so it makes too much hormone (hyperthyroidism). Symptoms can include weight loss, a racing heart, loose bowels, sweating, anxiety, poor sleep, shaky hands and lighter periods.

Once you have one autoimmune condition, you’re more likely to develop another. Hashimoto’s often occurs alongside coeliac disease, rheumatoid arthritis, lupus and Sjögren’s syndrome.

The gut and thyroid connection

Researchers now talk about a “gut-thyroid axis”. Your gut and your thyroid affect each other in both directions, and when one is out of balance, the other usually is too.

Dysbiosis and leaky gut. People with Hashimoto’s and Graves’ tend to have different gut bacteria to people without thyroid disease. When the microbiome is out of balance, the gut lining becomes more permeable and lets bacterial fragments into the bloodstream. This keeps the immune system on alert and can make thyroid autoimmunity worse. I explain this in more detail in How Your Gut Microbiome Drives Inflammation in Autoimmune Disease.

Nutrient absorption. Your thyroid depends on selenium, zinc, iron and iodine, and your gut bacteria play a key role in absorbing them. You can eat well and still be low if your gut isn’t absorbing properly.

Hormone recycling. Gut bacteria help reactivate thyroid hormone that the liver has packaged up for removal, so more of it goes back into circulation.

Medication absorption. Thyroid medication is absorbed in the small intestine. Coeliac disease, H. pylori infection, low stomach acid and inflammatory bowel conditions can all reduce how much you absorb. If your dose keeps creeping up, your gut is worth checking.

SIBO. A slow thyroid slows the gut, and a sluggish gut is a set-up for small intestinal bacterial overgrowth. A 2025 study found people with hypothyroidism were about twice as likely to develop SIBO, and the risk was higher again with autoimmune thyroiditis. This is one reason bloating and constipation are so common with Hashimoto’s.

Coeliac disease. Coeliac disease is more common in people with autoimmune thyroid disease. It damages the gut lining, affects nutrient and medication absorption, and is easy to miss because the symptoms can be subtle.

Testing: look at the thyroid and the gut

Thyroid symptoms overlap with so many other conditions that they’re easy to miss. A detailed personal and family history is often the first clue that the thyroid needs testing.

A full thyroid panel, not just TSH, should include:

• TSH: high usually means an underactive thyroid, low usually means an overactive one
• Free T4 and free T3: how much hormone is available, and how well you’re converting T4 into active T3
• Thyroid peroxidase antibodies (TPO Ab) and thyroglobulin antibodies (TgAb): raised in Hashimoto’s
• TSH receptor antibodies (TRAb): raised in Graves’ disease

Your doctor may also order a thyroid ultrasound to check for nodules or enlargement.

Gut testing is where we find out what’s driving the immune response:

• Microbiome stool testing to look at diversity, beneficial bacteria, inflammatory species and gut barrier markers
• SIBO breath testing if you have bloating, gas, constipation or reflux
• Coeliac screening through your GP, before removing gluten, because the blood test needs gluten in your diet to be accurate
• Nutrient levels such as iron studies, vitamin D and zinc

Test don’t guess. Two people with the same antibody levels can have very different things going on in their gut microbiome.

Where does AIP fit?

The Autoimmune Protocol (AIP) is an elimination and reintroduction diet. For a period of time, it removes foods that can trigger an immune response in some people (gluten and other grains, dairy, eggs, legumes, nightshades, nuts, seeds, refined sugar, alcohol and processed foods). The focus is on vegetables, quality protein and healthy fats. Foods are then brought back one at a time so you can see what you actually react to.

In a 10-week study of 17 women with Hashimoto’s, AIP significantly improved quality of life and symptoms, and lowered a marker of inflammation (hs-CRP). Thyroid antibodies didn’t change in that time. It’s a small study, but it supports what I see in practice. People often feel much better even when their medication dose stays the same.

AIP is a short-term tool, and the reintroduction phase is the most important part. Microbiome testing shows which beneficial bacteria are missing or low, which helps me prioritise the foods to bring back first. Fibre is usually the most important, because it feeds the bacteria that produce anti-inflammatory compounds like butyrate. Staying restricted for too long starves these bacteria, so a guided reintroduction is important.

Nutrients that support the thyroid

• Selenium: an analysis of 35 studies found selenium lowered TPO antibodies in people with Hashimoto’s. Brazil nuts are a rich source, but the amount varies a lot between nuts, so supplements should be dosed carefully.
• Zinc: needed to make thyroid hormone and convert T4 to T3.
• Vitamin D: helps regulate the immune system, and low levels are common in autoimmune disease.
• Iron: low iron stores can slow thyroid hormone production.
• Iodine, with care: the thyroid needs iodine, but too much can trigger or worsen Hashimoto’s. Don’t take iodine supplements or kelp without professional advice.

Stress, sleep and regular movement all matter too. Chronic stress affects both your thyroid and your gut, so it’s part of any plan I put together.

Ready to look deeper?

If you’ve been diagnosed with Hashimoto’s or Graves’ and you’re still struggling with fatigue, bloating, constipation or brain fog, your gut is a good place to start. I combine microbiome testing, SIBO breath testing (when needed) and a review of your pathology, then build a plan around what’s actually going on for you.

Book a discovery call here.

If you’re ready to understand your gut health a little better, follow along on Instagram. 💚

REFERENCES

Abbott RD, Sadowski A, Alt AG. Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus. 2019;11(4):e4556. doi:10.7759/cureus.4556. https://doi.org/10.7759/cureus.4556

Busto Silva I, Puig-Domingo M. The impact of thyroid disorders on the gut microbiome: emerging mechanisms and clinical relevance. Arch Endocrinol Metab. 2026;70(spec issue 1):e250075. https://pmc.ncbi.nlm.nih.gov/articles/12679698

Hughes K, Eastman CJ. Hashimoto’s thyroiditis: how to spot the diagnosis and how to manage it. Med Today. 2017;18(9):27-32. https://medicinetoday.com.au/mt/2017/september/feature-article/hashimotos-thyroiditis-how-spot-diagnosis-and-how-manage-it

Huwiler VV, Maissen-Abgottspon S, Stanga Z, et al. Selenium supplementation in patients with Hashimoto thyroiditis: a systematic review and meta-analysis of randomized clinical trials. Thyroid. 2024;34(3):295-313. doi:10.1089/thy.2023.0556. https://pmc.ncbi.nlm.nih.gov/articles/PMC10951571/

IBD is an immune-mediated condition that causes chronic inflammation in the digestive tract. The two main types are ulcerative colitis (UC) and Crohn’s disease (CD). There’s no single cause. Genetics, immune dysregulation, gut dysbiosis, a Western-style diet low in fibre and high in ultra-processed food, antibiotic use, smoking (for Crohn’s), stress and poor sleep can all play a part.

Research is also showing that UC may have a true autoimmune component. People who go on to develop UC can carry antibodies against integrin αvβ6, a protein that helps hold the gut barrier together, and these antibodies can appear up to 10 years before diagnosis. It’s another sign of how central the gut barrier is in IBD.

Ulcerative colitis and Crohn’s disease

UC and Crohn’s share many symptoms, including abdominal pain and cramping, diarrhoea, urgency, a feeling of incomplete emptying, blood or mucus in the stool, fatigue, poor appetite, weight loss and sometimes fever. Both follow a pattern of flares and remission, and both can range from mild to severe. They are still quite different conditions.

Ulcerative colitis affects the inner lining of the large intestine. It starts in the rectum and spreads upwards in one continuous stretch. The ulcers can bleed and produce mucus or pus, and ongoing blood loss can lead to iron deficiency anaemia.

Crohn’s disease can affect any part of the digestive tract, from the mouth to the anus, but most often involves the end of the small intestine (the ileum) and the colon. Inflammation can go through the full thickness of the bowel wall and appears in patches, with healthy sections in between. When the small intestine is affected, it can interfere with absorbing nutrients such as iron, vitamin B12, vitamin D and fats.

The gut microbiome in IBD

The gut microbiome is one of the most studied areas in IBD research, and the patterns are consistent. People with Crohn’s and UC tend to have:

• Lower diversity. Fewer different types of bacteria, which makes the gut ecosystem less resilient.
• Fewer butyrate producers. Bacteria like Faecalibacterium prausnitzii turn fibre into butyrate, which feeds the cells lining the bowel and helps calm the immune system. F. prausnitzii is often low in Crohn’s, and lower levels have been linked with a higher risk of the disease coming back after surgery.
• More inflammatory bacteria. Some species thrive in an inflamed gut and keep the immune system switched on.
• A weaker gut barrier. The protective mucus layer thins and the gut lining becomes more permeable, so bacteria come into closer contact with immune cells.

It becomes a cycle. Dysbiosis drives inflammation, and inflammation changes the environment in a way that favours more dysbiosis. I explain this process in more detail in How Your Gut Microbiome Drives Inflammation in Autoimmune Disease.

SIBO is common too. A 2025 analysis found around 31% of people with IBD had small intestinal bacterial overgrowth, much higher than in healthy people. The risk was higher after bowel surgery and in stricturing Crohn’s. SIBO can cause bloating, gas and diarrhoea that look a lot like a flare, so it’s worth testing when symptoms don’t match your inflammation markers.

Is IBD different from IBS?

Yes. The symptoms can look similar, but they are very different conditions.

IBD is driven by the immune system. It causes inflammation and damage to the gut lining that can be seen on colonoscopy and biopsy, and inflammation markers in the blood and stool are usually raised.

IBS is a disorder of gut-brain interaction. There’s no visible damage on colonoscopy and inflammation markers are usually normal. Gut sensitivity, motility changes, dysbiosis, SIBO, food triggers, stress and past gut infections can all play a part.

It’s possible to have both. Some people with IBD in remission still have IBS-type symptoms, which is why Microbiome testing is so important. Microbiome testing shows where the imbalance of bacteria is and we can then use selective prebiotics and probiotics to favourably change the composition of the gut microbiota.

How is IBD diagnosed and what happens next?

Diagnosis is done by your gastroenterologist who will use a combination of tests:

• Blood tests to check for inflammation (such as CRP), anaemia and nutrient deficiencies like iron, vitamin B12 and vitamin D
• Faecal calprotectin, a stool test that measures inflammation in the bowel and helps tell IBD apart from IBS
• PCR Stool tests to rule out infection
• Colonoscopy with biopsy, the main test for confirming IBD and telling UC and Crohn’s apart
• Gastroscopy if Crohn’s may be affecting the upper digestive tract
• MRI, CT, bowel ultrasound or capsule endoscopy to look at the small intestine, which a colonoscopy can’t fully reach

Gut testing

Once IBD is diagnosed, the next question is what’s driving the inflammation in your gut. This is what I look at starting with a detailed history: when your symptoms began, how severe they are, and what makes them better or worse. I then use:

• Microbiome stool testing to see your diversity, which beneficial bacteria are missing or low, which inflammatory species are overgrown, and markers of gut barrier health
• SIBO breath testing if bloating, gas or diarrhoea don’t match your inflammation markers
• A review of your pathology, especially iron, B12, vitamin D and zinc

Managing IBD with AIP

There’s no cure for IBD, but diet, targeted supplements and lifestyle changes can ease symptoms, reduce the severity of flares and help you stay in remission for longer. This works alongside your medical treatment, not instead of it.

The Autoimmune Protocol (AIP) is an elimination and reintroduction diet that can be very effective at reducing inflammation. Foods that can trigger an immune response in some people (gluten and other grains, dairy, eggs, legumes, nightshades, nuts, seeds, refined sugar, alcohol and processed foods) are removed for a short period of time. The focus is on nutrient-dense fruit and vegetables, quality protein and healthy fats. Foods are then brought back one at a time to see what you actually react to. Stress management, sleep and movement are part of the protocol too.

IBD was the first condition AIP was studied in. In a pilot study of 15 people with active Crohn’s or UC, 73% were in clinical remission by week 6, and they stayed in remission through the rest of the study. Most participants were still on their usual medication, so AIP was used as an add-on.

Reintroduction and fibre

AIP is a short-term tool, and the reintroduction phase is the most important part. Your microbiome results show which beneficial bacteria are missing or low, which helps me prioritise the foods to bring back first. Fibre is usually the most important, because it feeds the bacteria that make butyrate, and butyrate is one of the main things that helps settle inflammation in the bowel. We start with gentle, cooked and soluble fibres and build up slowly.

A note on strictures. If you have Crohn’s with a narrowed section of bowel, high amounts of insoluble fibre (raw vegetables, skins, seeds, nuts and tough fibrous foods) can raise the risk of a blockage. International IBD dietary guidance recommends limiting insoluble fibre in this situation, so your plan needs to be adjusted around it.

Other things that help

International dietary guidance for IBD also suggests:

• Eating more oily fish such as salmon and sardines for omega-3s
• Eating plenty of fruit and vegetables
• Cutting back on ultra-processed foods, especially those containing emulsifiers like carrageenan, carboxymethylcellulose and polysorbate-80
• Reducing red and processed meat

It’s also important to correct nutrient deficiencies, especially iron, vitamin B12, selenium, vitamin D and zinc, which are common in IBD.

Ready to look deeper?

If you’ve been diagnosed with Crohn’s or ulcerative colitis and you’re still dealing with flares, bloating, fatigue or unpredictable bowels, your microbiome is a good place to start. In my Gut Program, we combine microbiome testing, SIBO breath testing when needed and a review of your pathology, then build a plan around what your gut actually needs.

Living with IBD and want support? Book a consultation with me here: https://dashboard.healthbank.io/practitioner/vicky-ellenport

References

Feng X, Hu J, Zhang X. Prevalence and predictors of small intestinal bacterial overgrowth in inflammatory bowel disease: a meta-analysis. Front Med (Lausanne). 2025;11:1490506. doi:10.3389/fmed.2024.1490506. https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2024.1490506/full

Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221. https://doi.org/10.1097/MIB.0000000000001221

Levine A, Rhodes JM, Lindsay JO, et al. Dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2020;18(6):1381-1392. doi:10.1016/j.cgh.2020.01.046. https://doi.org/10.1016/j.cgh.2020.01.046

Livanos AE, Dunn A, Fischer J, et al. Anti-integrin αvβ6 autoantibodies are a novel biomarker that antedate ulcerative colitis. Gastroenterology. 2023;164(4):619-629. doi:10.1053/j.gastro.2022.12.042. https://pubmed.ncbi.nlm.nih.gov/36634824/

Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105(43):16731-16736. doi:10.1073/pnas.0804812105

#Inflammatoryboweldisease #Crohnsdisease #ulcerativecolitis #AIP #IBD #gutmicrobiome #clinicalnutritionist #personalisednutrition

Research suggests that increased intestinal permeability, often called “leaky gut”, may play a role in how some autoimmune conditions develop and progress.

The link between the gut and conditions like coeliac disease, Crohn’s disease and ulcerative colitis is easy to see. The connection to autoimmune conditions elsewhere in the body, such as type 1 diabetes, multiple sclerosis or rheumatoid arthritis, can be harder to picture.

So, let’s break it down.

What is the gut? Your digestive system and gut microbiome explained

“Gut” is another word for your gastrointestinal tract, or digestive system. Digestion begins in the mouth and continues in the stomach, but most food is broken down and absorbed in the small intestine. The large intestine absorbs water and electrolytes, and it is where gut bacteria ferment fibre into beneficial compounds called short-chain fatty acids. Waste is then expelled via the rectum.

The inner lining of the gut forms the intestinal barrier. It has several layers working together: a protective mucus layer, a single layer of cells joined by “tight junctions”, and immune cells sitting just beneath. The barrier is semipermeable. It lets nutrients, water and electrolytes through while keeping bacteria, toxins and other unwanted substances inside the gut to be excreted.

What is leaky gut? How intestinal permeability develops

The tight junctions between gut cells open and close in a regulated way. When the barrier is disrupted, these junctions loosen and the mucus layer can thin. This allows more to pass between the cells than should. This is known as increased intestinal permeability, or leaky gut. It can occur in both the small and large intestine.

What crosses is mostly bacterial products, such as lipopolysaccharide (LPS) from bacterial cell walls, along with toxins and fragments of food proteins. Immune cells beneath the lining recognise these as potential threats and respond, which creates inflammation.

Short-term, this is a normal protective response. However, when barrier disruption is ongoing, low-grade inflammation can persist and may contribute to wider health issues, including autoimmune disease.

What causes leaky gut? The main triggers that disrupt the intestinal barrier

1. Gluten. Gliadin, a protein found in gluten, can trigger the release of zonulin, a protein that temporarily loosens the tight junctions between gut cells. This response is strongest and most persistent in people with coeliac disease. Research suggests a smaller, short-lived effect may also occur in people without coeliac disease, including those with non-coeliac wheat sensitivity.
2. Dysbiosis. The gut microbiome plays a key role in keeping the barrier intact. Beneficial bacteria produce short-chain fatty acids such as butyrate, which fuel the cells of the gut lining and support tight junction integrity. When the microbiome is out of balance, these protective functions decline. A low-fibre diet can also shift bacteria towards feeding on the protective mucus layer, thinning the gut’s first line of defence. Bacterial overgrowth in the small intestine (SIBO) is another known trigger for zonulin release.
3. Elevated blood sugar. Persistently high blood glucose can reprogram the cells of the gut lining, weakening the junctions between them and allowing microbial products into circulation. In humans, poorer long-term glucose control (HbA1c) has been linked to greater leakage of microbial products. Diets high in sugar and fructose may also affect the barrier indirectly by altering the gut microbiome.
4. Stress. Psychological stress can increase gut permeability directly. Stress hormones such as corticotropin-releasing hormone (CRH) activate immune cells called mast cells in the gut wall, which loosens the barrier. Stress can also alter the gut microbiome over time. The effect appears to vary between individuals, and human research is still developing.
5. Alcohol. Alcohol and its by-product acetaldehyde directly disrupt the tight junctions between gut cells. Regular or heavy intake also promotes dysbiosis and bacterial overgrowth, which further weaken the barrier.
6. NSAIDs. Non-steroidal anti-inflammatory drugs such as ibuprofen, naproxen, diclofenac and aspirin are among the best-documented causes of increased gut permeability. They reduce protective prostaglandins in the gut lining and directly damage the energy-producing mitochondria in gut cells. Permeability can rise within hours of a single dose, and regular use commonly causes inflammation and injury in the small intestine

Leaky gut and autoimmune disease: how are they connected?

Autoimmune disease develops when the immune system loses “tolerance”, its ability to tell the body’s own tissues apart from genuine threats. Researchers think three factors often come together: a genetic predisposition, an environmental trigger, and a gut barrier that lets more through than it should.

When bacterial products and food proteins cross a disrupted barrier, the immune system is repeatedly activated. In someone who is genetically susceptible, this ongoing activation and inflammation may help tip the immune system towards attacking the body’s own tissues.

The outcome depends on the condition. In coeliac disease, gluten drives an immune response that damages the small intestine. In other autoimmune conditions, the immune response targets joints, the thyroid, the pancreas or the nervous system.

This model is well supported in coeliac disease. For many other autoimmune conditions, increased permeability is a likely contributor rather than a proven cause, and research is ongoing.

Can leaky gut improve? How gut microbiome testing helps

The gut lining renews itself every few days, so barrier function can improve when the factors disrupting it are addressed. For many people with autoimmune conditions, supporting gut health can help reduce inflammation, ease symptoms and improve quality of life, alongside their medical care.

Microbiome stool testing shows us what is actually happening in your gut: which bacteria are overgrown, which beneficial species are missing, and how that may connect to your symptoms. SIBO breath testing and a review of your pathology can add to the picture. From there, we build a targeted plan rather than guessing.

That plan may include microbiome-focused nutrition and supplements, stress and lifestyle support, and, where appropriate, a structured elimination and reintroduction approach such as the Autoimmune Protocol (AIP). Small studies of AIP in inflammatory bowel disease and Hashimoto’s thyroiditis have reported improvements in symptoms and quality of life.

5 natural ways to support leaky gut healing

1. Anti-inflammatory foods. Inflammation is a key driver of both leaky gut and autoimmune disease. Colourful fruit and vegetables, herbs and spices such as turmeric, and omega-3-rich oily fish (salmon, sardines, mackerel, anchovies, herring) all help. Plant foods contain polyphenols, which have anti-inflammatory properties and also feed beneficial gut bacteria.
2. Fermented foods. Fermented foods such as yoghurt, kefir, sauerkraut, kimchi and kombucha introduce live microbes and beneficial compounds. In one study, a diet high in fermented foods increased microbiome diversity and reduced markers of inflammation.
3. Prebiotic fibre. Prebiotics are fibres that feed beneficial bacteria, helping them produce barrier-supporting short-chain fatty acids. Good sources include onion, garlic, leek, asparagus, artichoke and green bananas. Many of these foods are high-FODMAP, so if you have IBS or SIBO, introduce them slowly or with guidance. Targeted prebiotic supplements can help if a high-fibre diet causes discomfort.
4. Glutamine. Glutamine is an amino acid that fuels the cells of the gut lining and supports tight junction integrity. In a clinical trial in people with post-infectious IBS, glutamine supplementation reduced symptoms and improved gut permeability. Food sources include meat, fish, eggs, dairy, tofu and legumes.
5. Reduce stress. Because stress directly affects the gut barrier, calming the nervous system is part of gut healing. Daily practices such as meditation, slow breathing or mindfulness can reduce stress, support sleep and help regulate immune function.

Gut health support for autoimmune conditions

If you’re living with an autoimmune condition or ongoing gut symptoms and want to understand what’s driving them, book a consultation. Together we’ll look at your gut microbiome, history and symptoms, and build a plan based on what your gut actually needs.

This article is general educational information and is not a substitute for individual medical advice. Please continue working with your GP or specialist for the management of any autoimmune condition.

References

Abbott et al. (2019) Efficacy of the autoimmune protocol diet as part of a multi-disciplinary, supported lifestyle intervention for Hashimoto’s thyroiditis. Cureus.11(4): e4556.

Bjarnason et al. (2018) Mechanisms of damage to the gastrointestinal tract from nonsteroidal anti-inflammatory drugs. Gastroenterology. 154(3):500–514.

Camilleri M. (2019) Leaky gut: mechanisms, measurement and clinical implications in humans. Gut. 68(8):1516–1526.

Chelakkot et al. (2018) Mechanisms regulating intestinal barrier integrity and its pathological implications. Exp Mol Med. 50(8):1–9.

Desai et al. (2016)A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 167(5):1339–1353.

Fasano A. (2020) All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability in the pathogenesis of some chronic inflammatory diseases. F1000Res; 9:F1000 Faculty Rev-69.

Konijeti et al.(2017) Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis. 23(11):2054–2060.

Kreimeyer et al. (2025) Influence of alcohol on the intestinal immune system. Alcohol Res. 45(1).

Maccioni et al. (2023) Alcohol-associated bowel disease: new insights into pathogenesis. eGastroenterology. 1(1):e100013.

Thaiss C et al. (2018) Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection. Science. 2018;359(6382):1376–1383.

Uhde et al.(2016) Intestinal cell damage and systemic immune activation in individuals reporting sensitivity to wheat in the absence of coeliac disease. Gut. 65(12):1930–1937.

Valitutti et al. (2019) Breaching the gut barrier: celiac disease as a paradigm of chronic inflammatory diseases. Dig Dis Sci. 64(7):1748–1758.

Vanuytsel  et al. (2014) Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans by a mast cell-dependent mechanism. Gut. 63(8):1293–1299.

Wastyk et al. (2021) Gut-microbiota-targeted diets modulate human immune status. Cell. 184(16):4137–4153.

A new study has found distinct differences in the gut microbiome of people newly diagnosed with multiple sclerosis (MS) compared with healthy individuals.

MS is an inflammatory, neurodegenerative autoimmune disease affecting the central nervous system. The immune cells mistakenly attack the myelin sheath surrounding nerve fibres, damaging nerves and disrupting nerve signaling.

About the study

Italian researchers used shotgun metagenomic sequencing to analyse stool samples from 53 adults with MS, recruited across four centres between 2017 and 2023, and 55 healthy controls. Patients were newly diagnosed, had not yet started disease-modifying therapies, and anyone who had used antibiotics in the previous three months was excluded. Almost half had received a short course of steroids at diagnosis, which the researchers accounted for in their analysis.

Which gut bacteria were linked to MS?

The gut microbiome differed significantly between people with MS and healthy controls:

• Barnesiella sp. An22 and Romboutsia ilealis were more abundant in MS and associated with a higher lesion burden.
• Clostridium innocuum and Ruminococcus sp. JL13D9 were more abundant in MS and associated with spinal cord lesions.
• Bacteroides species (B. ovatus, B. cellulosilyticus) were depleted, which may reflect reduced anti-inflammatory capacity. The MS microbiome also showed a reduced capacity to produce butyrate, an anti-inflammatory short-chain fatty acid.

Could microbiome testing help predict MS progression?

The researchers suggest that gut microbiome profiling at diagnosis may help identify patients at higher risk of faster disease progression and could offer new targets for microbiome-based interventions, though larger studies are needed to confirm this. They concluded that “incorporating microbiome analysis into clinical practice could contribute to more personalised management of MS.”

What this means for autoimmune gut health

In clinic, we often see that targeted microbiome modulation can help shift the gut ecosystem towards a more anti-inflammatory profile.

If you live with an autoimmune condition and want to understand how microbiome testing could inform your overall treatment, book a consultation with me in my Melbourne clinic or online.

References:
Maglione A, et al. (2026) Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study, eBioMedicine,132:106470. doi.org/10.1016/j.ebiom.2026.106470

Reflux, or Gastroesophageal reflux disease (GORD) is a chronic condition where stomach acid frequently flows back into the oesophagus, leading to mucosal damage and symptoms such as heartburn, regurgitation of food or acid, chest pain, chronic cough, difficulty swallowing and dental erosion.

There are many factors that contribute to the onset of GORD, the most common being reduced tone in the lower oesophageal sphincter (LOS). This can be caused by certain medications, such as NSAIDs, calcium channel blockers, barbiturates, and anticholinergics. Decreased saliva production and delayed stomach emptying are also contributing factors, as are lifestyle factors such as smoking, obesity, a diet high in fatty and processed foods, and alcohol consumption.

Gut dysbiosis contributes to both reflux and GORD symptoms and slow transit time and methane overgrowth can increase symptoms. Gut dysbiosis occurs when there is an imbalance between beneficial bacteria and harmful bacteria in the gut microbiome. Certain species of Proteobacteria and Fusobacteria produce lipopolysaccharides (LPS) which contribute to systemic inflammation and are thought to promote reflux by oesophageal sphincter relaxation. Research shows that high levels of Proteobacteria and Fusobacteria are more evident in people with GORD.

Conventional medicine includes proton pump inhibitors (PPI), H2 Receptor Antagonists (H2RAs) and other antacids which reduce stomach acid and can help with symptom management. However, they fail to address the cause of the reflux and are associated with many side effects such as diarrhoea, nausea, and abdominal pain. They also increase the risk of Small Intestine Bacteria Overgrowth (SIBO), Colonic Methane Overgrowth (CMO), nutrient malabsorption, and gut dysbiosis.

We use Microbiome testing to identify and treat any underlying drivers of reflux. We develop individual treatment plans based on your unique microbiome profile and your symptoms. Our holistic approach includes dietary and lifestyle recommendations and targeted supplements where necessary.

Here are a few of my recommendations.

Dietary modifications:

1. Eat a fibre-rich, plant-based, Mediterranean style diet.
2. Avoid trigger foods such as chocolate, fatty foods, and processed foods.
3. Avoid alcohol, sugar, and minimise coffee.
4. Have a 3-hour window between dinner and bedtime.
5. Do not consume fluid with meals or immediately after meals.

Lifestyle changes:

1. Elevating the head of the bed by 20-30 cm can reduce night-time reflux.
2. Stop smoking or vaping.
3. Reducing weight can alleviate symptoms.
4. Managing stress through breathing and nervous system support.

If you want to know more, please make an appointment or book in a discovery call.

REFERENCES:

De Bastiani et al. (2023) Assessment of small intestinal bacterial overgrowth and methane production in patients on chronic proton-pump inhibitor treatment: prevalence and role of rifaximin in its management in primary care. Minerva Gastroenterol 2023;69:523-8.
DOI: 10.23736/S2724-5985.21.03118-1

Baumeister et al. (2019) Gut microbiota and oesophageal disease – an update Microbiota Health Dis 1: e207 1 II.
DOI: 10.26355/mhd_20201_207

Cinnamon is known for its warm and sweet flavour, but it has a lot more to offer than its culinary applications. Cinnamon has been valued for centuries for its medicinal properties, and research shows it can be effective in reducing high blood pressure, regulating glucose levels, reducing inflammation, and improving cognition.

Cinnamon is rich in polyphenols, which are plant compounds known for their antioxidant properties. These polyphenols, including procyanidins and cinnamaldehyde, exhibit strong antioxidant activity, protecting cells from oxidative stress and damage caused by free radicals. Cinnamaldehyde has been shown to inhibit the release of pro-inflammatory cytokines in the gut, thus aiding in the reduction of gut inflammation and promoting gut health.

Cinnamon also exhibits prebiotic-like activity, supporting the growth of beneficial gut bacteria and suppressing the growth of pathogenic bacteria, positively impacting the balance of the gut microbiome. Several studies in healthy adults have demonstrated that cinnamon extract significantly increased the abundance of Bifidobacteria, Akkermansia and Lactobacillus, all known for their beneficial effects on gut health.

Studies have also shown that cinnamon oil can improve the oral microbiome by exhibiting a broad range of antimicrobial activity against the microbes causing dental caries. This is significant as dental caries is a risk factor for heart disease and Metabolic Syndrome.

Cinnamon also has many nutritional benefits. Adding one teaspoon (2-4 grams) of cinnamon powder a day provides calcium, potassium, vitamin A as well as small quantities of fibre and trace amounts of many other vitamins and nutrients.

So be bold and start adding cinnamon to your food and reap the benefits of its exotic taste whilst also supporting your gut microbiome and promoting optimal health.

REFERENCES

Jeong. et al. (2021). Antibacterial and antibiofilm activities of cinnamon essential oil nanoemulsion against multi-species oral biofilms. Sci Rep 11, 5911. DOI: 10.1038/s41598-021-85375-3

Kim et al. (2019). “Severity of dental caries and risk of coronary heart disease in middle-aged men and women: a population-based cohort study of Korean adults, 2002–2013.” Scientific Reports 9:10491 DOI: 10.1038/s41598-019-47029-3

Lu et al. (2019). “Mixed Spices at Culinary Doses Have Prebiotic Effects in Healthy Adults: A Pilot Study” Nutrients 11, no. 6: 1425. DOI: 10.3390/nu11061425

Lu et al. (2017). “Prebiotic Potential and Chemical Composition of Seven Culinary Spice Extract” Journal of Food Science Aug; 82(8): 1807–1813 DOI: 10.1111/1750-3841.13792

Mollazadeh et al. (2016). “Cinnamon effects on metabolic syndrome: a review based on its mechanisms.” Iran J Basic Med Sci. Dec; 19(12):1258-1270. DOI: 10.22038/ijbms.2016.7906.

Rao PV, Gan SH. (2014). “Cinnamon: a multifaceted medicinal plant.” Evid Based Complement Alternat Med. 642942. DOI: 10.1155/2014/642942

Vicky Ellenport BHSc NUT is a registered Nutritionist and Microbiome Analyst who uses a food first approach in her treatment protocols.

The process of getting an AID diagnosed can be so long, drawn out and frustrating that it is not uncommon for people with AID to be labelled a hypochondriac – a person who fears they are living with a serious, undiagnosed medical condition despite diagnostic tests showing that there is nothing wrong with them – especially in the early stages of illness.

On average, a person will see 5 doctors over the course of several years to finally receive an autoimmune disease diagnosis.

Autoimmune Disease Symptoms

While different autoimmune diseases affect different organs and systems in the body, what they all have in common is that they occur when the body’s immune system mistakenly attacks its own cells.

Autoantibodies are immune proteins that target the body’s own healthy tissue when the immune system fails to distinguish between “self” and “non-self”.

The continual attack on the body’s cells causes inflammation and sufficient tissue damage that symptoms of disease begin to emerge.

People with an autoimmune disease may describe long-term struggles with a wide range of symptoms such as: fatigue, gastrointestinal issues, joint pain, recurring infections, skin problems, allergies, migraines, unexplained weight changes, anxiety/depression, low/high blood pressure and more.

Why does it take so long to get an autoimmune disease diagnosis?

• Common, non-specific symptoms. The symptoms of autoimmune conditions vary widely and are generally non-specific, that is, symptoms that may describe any one of a variety of conditions. In the early stages of the illness people will usually present to their doctor or health professional for help with one, primary complaint (e.g., recurring urinary tract infection or persistent acne or inability to lose weight) and many of the other symptoms they are experiencing do not get mentioned. It is not until the practitioner has a full picture of ALL the symptoms, together with a full health history, that the connection between the symptoms becomes clearer, and that the possibility of an AID may become apparent.
• Remission/flare pattern. It is possible for an AID to enter a period of remission, where a person may have very mild symptoms, or even be asymptomatic, for a period. At this time, for an undiagnosed person, it may seem that the illness has resolved and is all but forgotten about. However, when triggered, AID can enter a flare phase when symptoms return suddenly and severely leaving the sufferer exhausted, depleted and in pain.
• Asymptomatic or slow to develop signs and symptoms. Not all Autoimmune Diseases cause symptoms immediately. It is possible to live with an AID for many years before symptoms become apparent or before an incident occurs that leads to an AID diagnosis. For example, ankylosing spondylitis symptoms may develop very gradually and often goes undiagnosed for several years, before it becomes visible on an x-ray. Likewise, Type 1 diabetes involves a gradual destruction of the pancreatic beta cells and it is only diagnosed once 90% of the cells have been destroyed.
• Co-Conditions. It is possible to have more than one AID, in fact having one AID increases the chances of you developing another. When there is more than one AID present, it is possible for one to mask the other. For example you may have been diagnosed with Rheumatoid Arthritis, but in actual fact you also may have Coeliac Disease, the symptoms of which contribute to joint pain, but remains undiagnosed if there are no other obvious symptoms.
• Every person is different and, with AID affecting a wide variety of organs and causing such varied symptoms, each presentation of each condition can be different. It is possible that two people may be diagnosed with the same condition with very different symptoms. Alternatively, two people with the same symptoms may be affected by different conditions.

Risk Factors for Autoimmune Disease.

Certain risk factors are known to increase the chances of developing an autoimmune disorder. The presence of any one of these risk factors, along with a description of all the symptoms, can help to get closer to an AID diagnosis.

• Genetics. While members of the same family may suffer from different autoimmune conditions, a predisposition to autoimmune disease does appear to run in families.
• Excess weight is associated with increased risk of developing an AID that affects the joints such as Rheumatoid and Psoriatic Arthritis. In addition, adipose tissue, or fat, secretes pro-inflammatory compounds that cause low-grade chronic inflammation and dysregulation of the immune system.
• Smoking. The toxic chemicals that are released when tobacco is burned impacts the immune system by causing inflammation, suppressing immune function, and stimulating the production of autoantibodies.
• Certain medications. The side effects of some pharmaceuticals that are widely used daily can have side effects that involve the immune system and can lead to an autoimmune reaction.
• Infection with a virus, such as Epstein Barr Virus (EBV), or bacteria, such as Streptococcus, can turn on genes that impede the immune system’s ability to differentiate between self and non-self, initiating an autoimmune reaction.

Are there tests for Autoimmune Disease?

There is no single test to diagnose AID but rather a selection of markers in blood or urine samples which, when put together with the presenting symptoms can lead to an AID diagnosis.

• Autoantibodies: The presence of autoantibodies may indicate an autoimmune disease.
  • Antinuclear Antibody (ANA) Test. A high level of these autoantibodies may be used to diagnose a systemic AID such as lupus and may be used to rule out other conditions with similar symptoms
  • Rheumatoid Factor (RF) is used to diagnose Rheumatoid Arthritis (RA). A positive test for RF differentiates RA from osteoarthritis and other connective tissue disorders.
  • Thyroid Antibody test (TPO) is used to diagnose Hashimoto’s or Graves disease in conjunction with other thyroid testing.
• Inflammation Markers: C-Reactive Protein (CRP) and Erythrocyte Sedimentation Rate (ESR) are used to detect the presence of inflammation, a common characteristic symptom of all AID’s.
• X-Rays, Gastroscopes and Biopsies: may be used to confirm or support an AID diagnosis.

Why do you need a diagnosis?

• Many people suffer with symptoms for many years and finally having a diagnosis can be a validation that it was not just in their mind.
• Knowing what is causing your symptoms allows your health practitioner to tailor a treatment plan specific to your needs.
• Having a diagnosis means that your health care team can anticipate, and help to reduce the risk, of disease progression or future complications.
• It helps you educate yourself and gain a better understanding about your condition and how to manage it.
• It reminds you that you are not alone, and that you can reach out and connect with others with the same condition so that you may support one another.

You have been diagnosed with an autoimmune disease, so what now?

Once you receive an AID diagnosis, the treatment approach is up to you. As there is no proven cure for AID, treatment is aimed at improving symptoms and promoting remission.

One option is the conventional medicine approach which prescribes pharmaceutical medications to manage symptoms and induce remission.

The other option is the natural medicine approach which aims to determine the underlying cause of your AID and to tailor a treatment plan to improve your symptoms and reduce the frequency of flare-ups.

As a natural medicine practitioner Vicky works in conjunction with your medical team, using a holistic approach to managing AID that encompasses thorough testing, identification of nutritional deficiencies, lifestyle and dietary recommendations and stress management techniques.

If you have been struggling with a long-term, undiagnosed health issue, or if you have recently been diagnosed with an AID, book in for a complimentary Discovery Session with Vicky to discuss the best options for managing your health.