How gut dysbiosis can trigger autoimmune liver disease

After working with hundreds of clients with autoimmune diseases - and seeing an increasing number with autoimmune liver conditions - I often look for patterns in their symptoms and test results. One recurring observation in my clients with autoimmune liver disease is gut dysbiosis, and the research backs this up.

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What is the link between gut dysbiosis and autoimmune liver disease?

Recent studies highlight the critical role of the gut microbiome in both the development and progression of autoimmune diseases, including autoimmune liver diseases (AILDs) such as:

  • primary biliary cholangitis (PBC)
  • autoimmune hepatitis
  • primary sclerosing cholangitis

Gut dysbiosis, an imbalance in the gut’s microbial community (both 'good' and 'unfriendly' organisms), has emerged as a potential factor in triggering the immune dysfunction that underlies these conditions.

The gut microbiome is home to trillions of bacteria, fungi, viruses, and other microorganisms that play a crucial role in digestion, immune function, and cellular health. Each type of microbe has a specific role, so when certain strains are lacking - or when harmful strains predominate - it can disrupt immune balance and contribute to a state of chronic inflammation.

In the context of autoimmune liver diseases, multiple studies have found a strong association between gut dysbiosis and liver inflammation, fibrosis, and other autoimmune-related damage. In this article, I’ll explore this link more deeply and discuss steps you can take to address it.


What is autoimmune liver disease?

Autoimmune liver diseases, including PBC, occur when the immune system mistakenly attacks the liver, causing inflammation, tissue damage and, in some cases, liver failure. Similar to other autoimmune conditions, these diseases likely result from a complex mix of genetic susceptibility, environmental factors, and immune system dysfunction.

PBC frequently affects women in their 40s or 50s and is often linked to other autoimmune conditions like thyroid disease or Sjögren’s syndrome. In my clinic, many women in this category have experienced prolonged stress, have been diagnosed with hypothyroidism, and are in perimenopause or menopause.

When we run a gut health test, nine times out of 10 they have severe dysbiosis, with overgrowths of bacteria such as Klebsiella and Citrobacter. While hormone dysregulation certainly appears to be part of the puzzle, growing evidence suggests that gut dysbiosis can tip the scales toward autoimmunity.

The gut-liver axis

The gut and liver share a complex relationship referred to as the 'gut-liver axis'. The gut microbiome helps regulate immunity by interacting with gut-associated lymphoid tissue (GALT), a central component of the immune system. An imbalance in the gut - often brought on by factors like antibiotic use, poor diet, or infections - can lead to dysregulation of immune responses, including potentially harmful attacks on the liver.

In diseases like PBC, this can mean an overly aggressive immune response that targets liver cells and bile ducts. Maintaining a balance of pro-inflammatory and anti-inflammatory microbes is key to preventing autoimmune activity. When the scales tip in the wrong direction, the risk of autoimmune reactions increases.

Another factor tying gut dysbiosis to autoimmune liver diseases is increased intestinal permeability (or 'leaky gut'). An imbalanced microbiome can compromise the gut lining, allowing bacteria, toxins, and undigested food particles to escape into the bloodstream. This can spark systemic inflammation and immune overactivity, ultimately affecting the liver.

In addition, many of my clients struggle with fat digestion, which can lead to the overproduction of lipopolysaccharides (LPS). LPS can be toxic in the body and may contribute to autoimmune liver disease.


Specific bacteria linked to autoimmune liver disease

When I run stool tests for clients, I often see clear indications of dysbiosis that may be driving or worsening their autoimmune conditions. Research has pinpointed several bacterial groups and species that appear to play critical roles in liver disease.

Firmicutes and Bacteroidetes

These are two major phyla that dominate the gut microbiome. Studies have noted that a decrease in Firmicutes (and thus fewer short-chain fatty acids with anti-inflammatory benefits) paired with an increase in Bacteroidetes can be linked to autoimmune liver diseases.

Lactobacillus and Bifidobacterium

These beneficial bacteria are known for helping maintain a healthy gut environment. They produce metabolites that reduce inflammation and enhance immune tolerance. Reduced populations of these microbes often correlate with increased gut permeability and inflammation, which can trigger autoimmune liver damage.

Faecalibacterium prausnitzii

An important member of the Firmicutes phylum, F. prausnitzii produces butyrate, a short-chain fatty acid known for its gut-protective and anti-inflammatory properties. Low levels have been associated with increased inflammation in autoimmune conditions, including PBC.

Clostridia strains

These support T regulatory (Treg) cells, which are vital for maintaining immune tolerance. A loss of these protective strains can impair Treg function, elevating the risk of autoimmune flare-ups in the liver.

Candida and parasites

Beyond bacteria, other organisms like candida (a naturally occurring yeast) and parasites can play a role in gut dysbiosis and autoimmune liver disease. Candida overgrowth, influenced by factors such as antibiotic use and chronic stress, has been associated with increased gut inflammation, intestinal permeability, and immune reactivity. Parasitic infections - commonly involving Giardia or Blastocystis - also disrupt the microbiome, further increasing inflammation and immune imbalance.

Although more research is needed to clarify precisely how parasites and fungi affect autoimmune liver disease, their impact on gut health and potential to trigger systemic inflammation is well-established.


What can you do to support gut and liver health?

The evidence linking gut dysbiosis to autoimmune liver disease makes it clear that supporting gut health is a critical step in managing these conditions. Here’s how to get started: 

1. Track symptoms

Start by tracking your digestive symptoms - bloating, pain, constipation, or general discomfort may point to an imbalance in your gut microbiome. A symptom journal covering your diet, stress levels, and lifestyle factors can reveal patterns and possible triggers.

2. Test your gut

If you suspect dysbiosis, a comprehensive stool test can uncover the composition of your gut flora, highlighting any harmful bacteria, parasites, or other issues.

3. Strengthen the gut lining

Once you have more information, focus on strengthening your gut lining and repopulating beneficial flora with targeted nutrients and dietary changes. L-glutamine, found in foods like cabbage soup and bone broth, can help restore the integrity of the gut lining. High-fibre foods (including stewed apples) and fermented foods support beneficial bacteria. Polyphenol-rich ingredients like cranberry or blackcurrant powder can enhance gut microbial diversity while providing antioxidant benefits.


By tracking your symptoms, investigating the state of your gut health, and nourishing your microbiome appropriately, you can take meaningful steps toward better gut and liver function. For those with autoimmune liver disease, these measures may help ease symptoms and slow disease progression. 

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The views expressed in this article are those of the author. All articles published on Nutritionist Resource are reviewed by our editorial team.

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London W1G & Harrogate HG1
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Written by V. J. Hamilton
Autoimmune Disease Expert | BSc (Immunology), DipION, mBANT
location_on London W1G & Harrogate HG1
After 25 years of suffering from multiple autoimmune conditions including alopecia, psoriasis and CFS, VJ discovered she could uncover the root cause of her issues to transform her health & live without symptoms. VJ now uses these same principles...
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