Around 90% of the body’s serotonin — often called the “feel-good” neurotransmitter — is produced in the gut, not the brain. This single fact changes the way most people think about mood, anxiety, and mental health.
The relationship between the gut and the brain is bidirectional, continuous, and increasingly well understood. It has a name: the gut-brain axis. And the state of your gut microbiome appears to be one of its key regulators.
What Is the Gut-Brain Axis?
The gut-brain axis is the communication network connecting the gastrointestinal tract and the central nervous system. It operates through three main channels:
- The vagus nerve — the longest nerve in the body, running from the brainstem to the abdomen. Around 80–90% of its fibres carry signals from the gut to the brain, making the gut one of the most significant sources of sensory information the brain receives.
- The enteric nervous system — sometimes called the “second brain,” this network of approximately 500 million neurons lines the gastrointestinal tract and operates largely independently of the central nervous system.
- The immune and endocrine systems — gut bacteria influence the production of hormones and immune signalling molecules that circulate systemically and affect brain function.
A comprehensive review published in Physiological Reviews (Cryan et al., 2019) — one of the most cited papers in the field — described the microbiota-gut-brain axis as a fundamental regulatory system affecting behaviour, cognition, and stress response.
How the Gut Microbiome Influences the Brain
Neurotransmitter production
Gut bacteria produce or regulate the production of several key neurotransmitters. Around 90–95% of the body’s serotonin is synthesised in the gut by enterochromaffin cells, a process regulated in part by the microbiome. Gut bacteria also contribute to the production of GABA (gamma-aminobutyric acid), which has inhibitory — calming — effects on the nervous system, and dopamine precursors.
This doesn’t mean gut-produced serotonin directly enters the brain — the blood-brain barrier prevents this. But gut serotonin regulates gut motility, plays a role in pain sensitivity, and signals through the vagus nerve to the brain, influencing mood indirectly.
Short-chain fatty acids and brain function
When gut bacteria ferment dietary fibre, they produce short-chain fatty acids (SCFAs) including butyrate, propionate, and acetate. These compounds cross the blood-brain barrier and have direct effects on brain function — including reducing neuroinflammation and influencing the production of brain-derived neurotrophic factor (BDNF), a protein associated with learning, memory, and mood regulation.
The immune-inflammation pathway
Chronic low-grade inflammation — driven in part by gut microbiome disruption — is increasingly implicated in depression and anxiety. A disrupted gut microbiome increases intestinal permeability, allowing bacterial compounds to enter the bloodstream and trigger systemic immune responses. These inflammatory signals reach the brain and can affect mood, cognition, and stress resilience.
The Gut-Brain Axis and Mental Health
Depression and anxiety
Multiple studies have found associations between gut microbiome composition and mental health conditions. A study published in Nature Communications (Valles-Colomer et al., 2019), analysing data from over 1,000 participants, found that people with depression had lower levels of Coprococcus and Dialister bacteria — species associated with quality of life and mental wellbeing. Coprococcus is involved in dopamine metabolism, suggesting a direct mechanistic link.
The direction of causality is still being studied — it’s not yet clear whether poor gut health causes depression or whether depression alters gut health, or both simultaneously. The current evidence suggests the relationship is bidirectional.
Stress and the gut
Stress is one of the most well-established disruptors of gut microbiome health. When the body activates the stress response, resources are diverted away from digestion, gut motility changes, and the composition of the microbiome can shift within days.
Research published in the Journal of Neuroscience (Mayer et al., 2014) established that psychological stress alters gut microbiota composition, which in turn affects mood and stress resilience — a loop that can compound over time. This is why people with chronic stress often experience persistent gut symptoms, and why people with gut disorders often experience elevated anxiety.
Cognitive function and ageing
Emerging research links gut microbiome diversity to cognitive performance, particularly in older adults. The gut-brain axis may be relevant to age-related cognitive decline — microbial diversity tends to decrease with age, and SCFAs like butyrate have demonstrated neuroprotective effects in animal studies. Human trial data is still limited, but the mechanistic pathway is plausible.
What This Means Practically
The gut-brain axis provides a physiological basis for what many people experience intuitively: poor gut health tends to accompany low mood, fatigue, and reduced stress resilience. And interventions that improve gut health — particularly dietary changes — often have effects that extend beyond digestion.
The most evidence-backed approaches for supporting the gut-brain axis are the same foundations that support gut health generally:
- Fermented foods — a 2021 Stanford study found fermented food diets reduced inflammatory markers significantly, which has downstream implications for brain health
- Dietary fibre diversity — supports SCFA production, which has direct effects on brain function via the blood-brain barrier
- Stress management — reduces the feedback loop between stress and gut disruption
- Consistent sleep — both the brain and the gut operate on circadian rhythms; disrupting one disrupts the other
- Probiotic and fermented supplementation — specific strains including Lactobacillus rhamnosus have been studied in the context of anxiety and stress response
For a broader look at how to support gut health through diet and supplementation, see our guide to gut health. If you’re looking for a supplement designed around fermented delivery of multiple probiotic strains, Biome Bliss combines probiotics, prebiotics, and postbiotics in a naturally fermented tonic format.
Frequently Asked Questions
What is the gut-brain axis?
The gut-brain axis is the bidirectional communication network between the gastrointestinal tract and the central nervous system. It operates via the vagus nerve, the enteric nervous system, and immune and hormonal signalling. The gut microbiome is a key regulator of this system, influencing neurotransmitter production, inflammation, and stress response.
How does gut health affect mood?
Gut bacteria produce or regulate the production of neurotransmitters including serotonin and GABA. They also produce short-chain fatty acids that cross the blood-brain barrier and influence brain function. A disrupted microbiome increases systemic inflammation, which has been associated with depression and anxiety.
Can improving gut health help with anxiety?
The evidence is promising but not definitive. Several studies link gut microbiome composition to anxiety levels, and interventions that improve gut health — particularly fermented foods and fibre diversity — are associated with reductions in inflammatory markers that may contribute to anxiety. Specific strains such as L. rhamnosus have been studied in this context. More human trial data is needed before firm conclusions can be drawn.
What is the vagus nerve’s role in gut-brain communication?
The vagus nerve is the primary physical connection between the gut and the brain. Approximately 80–90% of its fibres carry signals from the gut to the brain rather than the other way around, making the gut one of the most significant sources of sensory input the brain receives. It transmits signals about gut conditions — including inflammation and microbiome activity — directly to the brainstem.
Does stress damage gut health?
Yes. Chronic stress alters gut microbiota composition, reduces microbial diversity, and increases gut permeability. The gut and brain are connected in a feedback loop — a disrupted gut amplifies stress response, and chronic stress further disrupts the gut. Managing stress through sleep, exercise, and structured downtime is directly relevant to gut health, not just mental wellbeing.
References
- Cryan JF et al. (2019). The microbiota-gut-brain axis. Physiological Reviews, 99(4), 1877–2013. pubmed.ncbi.nlm.nih.gov/31460832
- Valles-Colomer M et al. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4(4), 623–632. pubmed.ncbi.nlm.nih.gov/30718848
- Mayer EA et al. (2014). Gut microbes and the brain: paradigm shift in neuroscience. Journal of Neuroscience, 34(46), 15490–15496. pubmed.ncbi.nlm.nih.gov/25392516
- Wastyk HC et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137–4153. pubmed.ncbi.nlm.nih.gov/34256014
This article is for informational purposes only and does not constitute medical advice. If you are experiencing persistent symptoms affecting your mood or digestive health, please consult a GP or registered healthcare professional.
