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The Gut-Brain Axis: Exploring the Microbiome’s Role in Mental and Physical Health

Written by Kaitlin Colucci, Consultant Gut Health Dietitian

Reading time: 10 minutes

When we think about health, we often separate the mind from the body, but science is revealing just how interconnected they truly are. At the heart of this connection lies the gut-brain axis, a complex, bidirectional communication system linking the gut and the brain. But at the centre of it all, is the gut microbiome, the trillions of microbes living in our digestive tract and primarily the large intestine, which do far more than just support digestion. The emerging field of research around the gut microbiome is transforming how we understand gastrointestinal disorders, mental health, and the intricate balance between diet, lifestyle, and overall health.

Understanding the Gut-Brain Axis

The gut-brain axis is a bi-directional communication system between the enteric nervous system (ENS), which is found in the lining of the gastrointestinal tract (aka ‘the gut’), and the central nervous system (CNS) (‘the brain’), connected primarily via the vagus nerve (though other communication pathways exist such as via the neuroendocrine system). The enteric nervous system allows the gut to function somewhat independently of the brain, earning it the nickname ‘the second brain’.[1]

The enteric nervous system has two key arms:

Parasympathetic Nervous System (PNS):

• Often referred to as the "rest and digest" system

• Activated when the body is calm and relaxed, promoting digestion and gut motility
  .

Sympathetic Nervous System (SNS):

• Known as the "fight or flight" system

• Activated during stress, redirecting blood flow away from the gut to prepare the body for action[2]
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However, this communication system can become disrupted under stress. Whether it’s facing an urgent deadline, missing a train, or feeling overwhelmed with responsibilities, chronic stress keeps the body in a prolonged state of sympathetic activation. This shift can lead to slower digestion, irregular bowel movements, or heightened gut sensitivity, contributing to bloating, discomfort, and even increased bowel urgency.[3]

Over time, chronic stress can also weaken the gut barrier, making it more permeable, a phenomenon sometimes called “leaky gut”. This allows inflammatory molecules to enter the bloodstream, further exacerbating gut-related symptoms and can contribute to systemic inflammation.[4] On the flip side, when the body is relaxed, the parasympathetic nervous system supports normal digestive function, allowing regular gut motility to resume.[5]

How the Gut Microbiota Influences Brain Function

Beyond the structural connections of the gut-brain axis, the gut microbiota itself plays a key role in neurotransmitter and neurotransmitter precursor production. For example, approximately 90% of the body's serotonin is synthesised in the gut. However, neurotransmitters produced in the gut cannot cross the blood-brain barrier, therefore the role of gut-produced serotonin is largely to support normal gut motility.

It is now believed that the impact of the gut microbiota on brain function/mood may be through direct interaction of gut-produced neurotransmitters via the vagus nerve/ENS, or, critically, through regulating the metabolism and production of neurotransmitter precursors (typically amino acids), which can cross the blood brain barrier and may support brain synthesis of neurotransmitters. For example, metabolites of colonic fermentation by the microbiota - such as acetate - can cross the blood-brain barrier and be utilised in the GABA (Gamma-Aminobutyric Acid) metabolic cycle. Indicating that the gut microbiome can directly and indirectly impact brain activities and cognitive functions.[6]

The gut is also home to approximately 70% of the body's immune cells.[7] The microbiome helps regulate immune function by interacting with gut-associated lymphoid tissue (GALT), which plays a key role in distinguishing harmful invaders from beneficial microbes. A compromised gut barrier due to stress, poor diet, or infections allows inflammatory molecules, like cytokines, into the bloodstream, which can impact brain function. Chronic inflammation has even been linked to mental health conditions like depression and anxiety, further reinforcing the gut-brain connection.[8]

The Role of Diet in Supporting the Gut-Brain Axis

Diet plays a crucial role in shaping the gut microbiome and, in turn, support normal brain health. One of the most important nutrients that does this is dietary fibre.

Fibre forms the backbone of all our plant-based foods. These include fruits, vegetables, whole grains, legumes, nuts, and seeds. When we consume fibre, our gut bacteria ferment it, producing short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate, which are essential for gut-brain communication.[9]

Butyrate, in particular, supports dopamine production, the neurotransmitter involved in motivation, mood, and focus. It also helps reduce inflammation and maintain the integrity of the blood-brain barrier[10]

SCFAs also interact with the enteric nervous system, influencing gut motility and overall digestive health

How Fermented Foods and Probiotics may Impact Brain Function

Eating fermented foods which contain a wide variety of live cultures like yogurt, kombucha, tempeh, sauerkraut, and kimchi helps maintain a diverse gut microbiome, which, in turn, influences brain function through the production of SCFAs.[11]

Certain foods may include specific probiotics that are supported by clinical research and have been proven to survive and reach the gut. For example research by Tillisch et al. (2013) showed that consuming fermented foods with probiotics (specifically, two daily 125g servings of Activia yogurt) was associated with changes in brain activity in regions linked to emotions and sensory processing.[12] This suggests that probiotic foods may have the potential to influence mood and stress responses via the gut-brain axis.

Alongside probiotics, prebiotics (found in bananas, garlic, and onions) feed beneficial gut bacteria, encouraging SCFA production, while postbiotics (the beneficial byproducts of probiotics) reduce inflammation and promote neuroprotection.[13]

The Role of Psychobiotics in Mental Health

Psychobiotics are a special category of probiotics that may support mental health. Whilst evidence in this space is still being explored, these specific live bacteria may influence the gut-brain axis by a number of purported mechanisms:

• Stimulating the vagus nerve, which sends signals from the gut to the brain

• Regulating the metabolism of neurotransmitter precursors such as tryptophan[14]

• Production of other neuroactive compounds, such as melatonin
  .

Emerging research suggests that specific strains, like Lactobacillus and Bifidobacterium, can help regulate mood and reduce symptoms of anxiety and depression. Studies have even shown that Bifidobacterium longum and Lactobacillus helveticus supplementation was linked to lower cortisol levels, suggesting their potential role in stress management.[14]

While the field of psychobiotics is still evolving, the evidence points to probiotic-rich foods or supplements as a natural approach to supporting mental well-being. When combined with a gut-nourishing diet and stress management strategies, they offer a powerful tool for both digestive and mental health.

Holistic approaches

The gut and brain are constantly in conversation, sending signals back and forth through nerves and chemical messengers. The gut regularly updates the brain on what’s happening inside, whether it’s feeling full after a meal or sensing the need for a bowel movement. Most of the time, the brain processes these messages subconsciously, similarly to how you eventually stop noticing the sensation of wearing a watch after a while. The brain also plays an active role in regulating gut function, adjusting fluid levels, acid production, and motility to aid digestion.

However, sometimes this communication system gets disrupted. The brain may start interpreting gut sensations more intensely, or it might send inappropriate signals back down, disrupting normal digestion and gut function. The good news is that since the brain has a powerful influence over the gut, we can use brain-body practices to restore balance. Techniques like yoga, meditation, and breathwork have been shown to positively impact gut health by calming the nervous system and improving gut motility.[15] In fact, the NICE guidelines on the management of irritable bowel syndrome now recognise psychological interventions such as cognitive behavioural therapy (CBT) and hypnotherapy as important interventions for those who have not responded to dietary and pharmacological interventions.[16]

• Breathwork: Deep breathing exercises help activate the parasympathetic nervous system, and research has shown that slow, controlled breathing can positively affect gut motility and reduce stress-related gut symptoms[17]

• Yoga: Yoga and meditation influence vagal tone, the activity of the vagus nerve, which connects the gut and brain. Studies have found that these practices can lower stress levels and reduce symptoms of irritable bowel syndrome (IBS) by modulating gut-brain interactions[18]

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Conclusion

The gut and brain are deeply intertwined, constantly communicating through a complex network of nerves, neurotransmitters, and immune signals. What happens in the gut doesn’t stay in the gut, it directly and indirectly impacts mood, cognition, and mental health. By nurturing our gut microbiome through diet, lifestyle, and stress management, we can support both digestive and mental health in a meaningful way.

Here are five key takeaways to help optimise your gut-brain connection:

• What you eat shapes your gut and brain health – A diet rich in fibre, fermented foods, and prebiotics can help support a diverse gut microbiome, which may regulate the gut-brain axis to support normal mood and cognition

• Your gut produces key brain chemicals – The gut microbiota plays a major role in producing neurotransmitters, neurotransmitter precursors and other neuroactive compounds which can directly or indirectly influence mood

• Psychobiotics may support mental health – Specific probiotic strains, such as Lactobacillus and Bifidobacterium, may have a role to play in supporting mental health due to their influence on the gut-brain axis

• Stress impacts digestion – Chronic stress keeps the body in a “fight or flight” state, disrupting gut motility, increasing gut permeability, and contributing to symptoms like bloating, discomfort, and irregular bowel movements

• Mind-body practices can improve gut function – Techniques like yoga, meditation, and breathwork help activate the vagus nerve, and help regulate the gut-brain axis and support normal gut function

By adopting a holistic approach, combining nourishing foods, stress management, and movement, you can support both gut and brain health, improving your overall energy, mood, and resilience. The science of the gut-brain axis is still evolving, but one thing is clear: a healthy gut is key to a thriving mind.

Would you like to learn more? Start by incorporating gut-friendly foods into your diet and exploring mind-body practices to support your gut-brain connection. Visit www.themissiondietitian for further guidance and support.

If your patients want to learn more about how their own lifestyle may impact their gut health, you can direct them to the Activia Gut Health Tracker , which provides guidance on simple changes to help support their gut health.