The Gut-Brain Axis

The brain influences how our microbiota develops over time and also its composition.

In turn, microbes influence metabolism and mental health.

The brain and microbes communicate via:

  • The immune system
  • Endocrine function
  • Neural pathways

How do microbes get messages to our brain?

  1. Immune cells sense bacteria and release cytokines which affect brain function
  2. Cells in the intestinal walls produce peptides (short amino-acids chains) and peptides can activate nerve endings
  3. Microbes produce direct signals called neurotransmitters (signalling molecules used by the nervous system

Microbes can make chemicals that speak the brain’s language

90% of the serotonin in our bodies is produced in the gut and only 10% in the brain

Under stressful conditions the brain releases corticosteroids which affect the immune cells in the gut and also its permeability. Therefore when we are stressed, microbes can leak out of the gut

The brain can also change which microbes are in the gut. Neurotransmitters directly affect the composition of gut microbial communities

Behavioural changes

We know that microbes affect the behaviour of mice, for instance:

  • Obese mice – alterations in eating patterns
  • Aggressive mice – probiotics made them less aggressive


Different microbes appear in the gut but causality is unclear. It is harder to prove because changes in microbes appear alongside gut barrier dysfunction seen in autistic children. Microbes, metabolites (substance produced by metabolism) and health are all linked. We need to:

  1. Identify altered microbial profiles and metabolites
  2. Conduct pre-clinical trials
  3. Carry out clinical trials on humans

There is an association between autism and gastro intestinal problems. The literature is

conflicting though.


Stress is linked to changes in gut microbes. Normal gut microbes may increase resilience to stressful conditions.



This is linked to the immune system and therefore makes sense if we manipulate the microbiome we may be able to alter depression, stress and anxiety.

Mycobacterium vaccae which is a microbe found in soil decreases anxiety in mice

We may be able to vaccinate against depression with microbes or take probiotic supplements such as Lactobacillus and Bifidobacterium (produced in short chain fatty acid production) to decrease stress.

The immune system and the nervous system both have a memory and there is an overlap in how the two systems work. If microbes impact the immune system then they must impact the nervous system. 70% of periphery neurons are in the gut.

Microbes have direct access to the nervous system. Gut microbes impact the development and function of the immune system.

A species of intestinal bacteria called Bacteroides fragilis produces a sugar molecule called polysaccharide A (PSA). This is known to improve the function of T-cells.

The adaptive immune system becomes activated and leads to tissue damage causing auto immune disease. There needs to be a balance of pro-inflammatory cells and anti-inflammatory cells. Microbial molecules can activate anti-inflammatory response so if we can harness this we can boost this with PSA and use it to treat inflammatory bowel disease and MS. See this article for further information.



The Human Microbiome Course

What is a Microbe?

The Human Microbiome

How we study the Microbiome Part 1

How we study the Microbiome Part 2

Impacts on the Microbiome

Microbiome and Obesity

The gut microbiota, autoimmune diseases and allergies

Human Microbiota and Gut Disease

Interactions between the Gut Microbiota and Immune System

The Gut-Brain Axis

Useful website articles and links

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