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. 💚

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.

Autoimmune disease is a malfunction of the immune system.

The fundamental role of the immune system is to protect the body from invading pathogens such as viruses and bacteria. In Autoimmune Disease (AID), the immune system mistakenly recognizes the body’s own tissues as a threat and produces autoantibodies. This results in inflammation and damage to cells, tissues and organs which can impair normal functioning.

Autoimmune Conditions

Autoimmune disease affects around 5% of Australians and there are around 80 different known autoimmune conditions, with many more diseases that are suspected to be autoimmune in origin. Many are difficult to diagnose and even more difficult to treat. Most autoimmune diseases are chronic and lifelong, and their incidence is increasing year on year in most countries around the world.

Some of the more common autoimmune diseases include: Coeliac Disease, Rheumatoid Arthritis, Multiple Sclerosis, Hashimoto Thyroiditis, Type 1 Diabetes, Inflammatory Bowel Disease (including Ulcerative Colitis and Crohn’s Disease) and Psoriasis. Fibromyalgia and Chronic Fatigue Syndrome are conditions that are suspected to have autoimmune origins.

Why does the Immune System malfunction?

Though the exact causes of autoimmune disease remain unknown, there are certain risk factors that increase the chances of developing an autoimmune condition.

Genetics accounts for approximately one third of this risk, while the remaining risk is thought to come from environmental triggers such as exposure to pollution, toxins, viruses, intestinal dysbiosis (causing leaky gut) and diet and lifestyle factors.

So what does this mean for you?

This means that autoimmune disease is directly linked to your food choices and how you choose to live your life. What this suggests is that you can manage your autoimmune disease by changing your diet and making more informed choices about sleep, activity, and stress.

The Autoimmune Protocol

The Autoimmune Protocol (AIP) is a comprehensive program which focuses on diet and lifestyle factors known to be important modulators of immune function. Healing is supported by the removal of inflammatory stimuli to reduce the chronic inflammation that causes tissue damage.

That may seem like a lot to ‘digest’, so a certified AIP practitioner can help you put this into practice.

The Autoimmune Protocol provides guidelines for both diet and lifestyle changes to successfully manage the symptoms of autoimmune disease.

About the AIP Diet

The AIP diet consists of an elimination strategy, cutting out the foods that are most likely to be holding back our health. After a period of time, many of the excluded foods, especially those that have nutritional merit, can be reintroduced.

The AIP diet provides balanced and complete nutrition by prescribing nutrient dense foods while avoiding processed & refined foods.

The AIP Lifestyle

Lifestyle factors including high stress, poor sleep and minimal activity can contribute to inflammation and increase the risk of immune dysfunction leading to the onset or flare up of autoimmune disease.

The AIP provides strategies for improved sleep, stress management and regular physical activity as these are important immune modulators and are key to successfully managing AID.

Is this lifestyle difficult to maintain?

Autoimmune diseases are difficult to manage and at times can feel out of control.

By adopting diet and lifestyle strategies, such as the Autoimmune Protocol, the frequency and severity of symptoms may be reduced and quality of life improved.

If you are someone who has been recently diagnosed with an AID, or maybe you have been struggling to manage your AID for some time, the Autoimmune Protocol is for you. Book in for a Complimentary Discovery Session with Vicky to find out more. https://thenutritionfactor.com.au/book-appointment/