Can Poor Gut Health Cause Anxiety and Depression? What the Research Says
Written by Jessica Diakoumakos, Naturopath (BHSc Naturopathy) · Emba Wellness, Melbourne · Updated 14.04.2026
Research shows a clear relationship between gut dysbiosis and mood disorders including anxiety and depression. The gut microbiome influences neurotransmitter production, regulates cytokine activity and neuroinflammation, and modulates the HPA axis stress response. Addressing gut health is increasingly recognised as a meaningful component of a comprehensive mental health approach — particularly when symptoms haven't fully resolved with other interventions.
One of the most common things I hear from new clients is some version of:
"I've been managing my anxiety for years, I've tried everything, and I still don't feel right."
What they've often never been asked is: how's your gut?
Not as a throwaway question — but as a genuine clinical inquiry. Because the research connecting gut dysbiosis to anxiety, depression, and altered stress responses is now substantial. And in practice, when I start looking at gut function in clients with persistent mood concerns, I almost always find something.
This post is the clinical companion to my earlier piece on the gut-brain axis. If you haven't read that yet, [start there →]— it covers the foundational science of how the gut and brain communicate. Here, we go into what happens when that communication breaks down, and what a naturopathic approach to gut-brain health actually looks like.
The Immune System, Cytokines, and Brain Inflammation
Your gut houses around 70% of your immune system. The bacterial composition of your microbiome has a significant influence on how your immune system behaves — including the production of cytokines, the signalling proteins that regulate inflammation throughout the body.
When the microbiome is balanced, cytokine production is regulated and inflammation is kept in check. When there's dysbiosis — an imbalance in the microbial community — cytokine activity can become dysregulated, contributing to both systemic and neurological inflammation.
Neuroinflammation is increasingly being recognised as a significant driver of depression and anxiety. Research by Park et al. (2025) in Cellular & Molecular Immunology shows that disruption to gut microbiota composition and barrier integrity has been implicated in neurological and psychiatric conditions including depression, anxiety, and neurodegenerative diseases.
This doesn't mean poor gut health directly causes these conditions — but it does mean that addressing gut dysbiosis can be a meaningful part of a comprehensive approach to mental health support, particularly in treatment-resistant cases.
The HPA Axis and Your Stress Response
The hypothalamic-pituitary-adrenal (HPA) axis is the system that governs your stress response — controlling the release of cortisol and other stress hormones. And your gut microbiome has a direct influence on how this system functions.
Research by Kurhaluk et al. (2025) in the International Journal of Molecular Sciences describes how the gut microbiota and vagus nerve interact to form a bidirectional neuroimmune network that modulates the HPA axis, immune function, and neurotransmitter balance. When the microbiome is healthy and diverse, it helps regulate the HPA axis and supports a measured, proportionate stress response. When there's dysbiosis, HPA axis activity can become dysregulated — contributing to elevated cortisol, heightened anxiety, and a reduced capacity to recover from stress.
This is why I frequently see clients whose anxiety or stress response seems disproportionate to their circumstances. When we look at their gut health — through microbiome analysis or functional testing — there's often something going on at the microbial level that's contributing to how they're experiencing and processing stress.
“In clinic, the gut-brain connection is one of the first things I consider when someone comes to me with mood concerns alongside gut symptoms — or even when they don’t. The research is clear that these systems are not separate. When we address gut dysbiosis, support microbiome diversity, and reduce intestinal inflammation, we’re often doing meaningful work for brain health at the same time”
What This Means Clinically
The gut-brain connection has real, practical implications for how we approach mood, mental health, and stress resilience.
If you're dealing with anxiety, low mood, or brain fog — your gut health is worth investigating, especially if conventional approaches haven't given you full relief. This isn't about abandoning other treatments. It's about asking whether there's a gut-level driver that's being missed.
If you're dealing with gut symptoms like IBS, bloating, or dysbiosis — the impact on your mood and mental clarity is real and measurable. These are not separate problems running in parallel. They're often the same problem expressing itself in two places at once.
If you've taken antibiotics recently or have a history of gut disruption — rebuilding a diverse, resilient microbiome supports not just digestion, but your neurological and emotional health too.
What a Naturopathic Approach Looks Like
Gut-brain health is an area where naturopathic medicine has a lot to offer — not because it replaces conventional mental health care, but because it sits in the space conventional medicine often doesn't have time for: the functional assessmentof what's actually driving the imbalance.
In practice, this means:
Functional Testing
Microba microbiome profiling, SIBO breath testing, and comprehensive functional blood panels can reveal specific drivers that standard pathology won't pick up. If your bloods have been "normal" but you still feel terrible, functional testing often tells a different story.
Microbiome Restoration
Using evidence-based probiotic and prebiotic therapy, targeted dietary changes, and herbal medicine to rebuild microbial diversity and reduce dysbiosis. This is an area I've trained in specifically with Dr Jason Hawrelak at the Microbiome Restoration Center.
HPA Axis Support
Addressing the stress-gut feedback loop through adaptogenic herbal medicine, nutritional support for the adrenal and nervous systems, and lifestyle interventions that reduce the chronic stress burden on the microbiome.
Dietary and Lifestyle Foundations
A diverse, high-fibre diet is one of the most evidence-based interventions for microbiome health. But what that looks like is highly individual — food intolerances, gut infections, and conditions like SIBO mean that what's helpful for one person can be actively harmful for another.
Frequently Asked Questions
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Research shows a clear relationship between gut dysbiosis and mood disorders including anxiety and depression. Gut bacteria influence neurotransmitter production, regulate the HPA stress axis, and modulate neuroinflammation — all of which affect mental health. While gut dysbiosis is unlikely to be the sole cause of these conditions, addressing gut health can be a meaningful part of a comprehensive treatment approach, particularly when symptoms haven't fully resolved with other interventions.
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Gut dysbiosis is an imbalance in the composition of the gut microbiome — typically involving a reduction in microbial diversity and an overgrowth of less beneficial species. Dysbiosis disrupts neurotransmitter production, impairs short-chain fatty acid synthesis, increases intestinal permeability, and dysregulates immune and cytokine activity. These downstream effects can contribute to neuroinflammation and altered brain function, which are increasingly linked to anxiety and depression.
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The hypothalamic-pituitary-adrenal (HPA) axis is the body's primary stress response system, governing cortisol production and the fight-or-flight response. The gut microbiome modulates HPA axis activity through the vagus nerve and immune signalling. A balanced microbiome supports a proportionate, regulated stress response. Dysbiosis can dysregulate the HPA axis, leading to elevated cortisol, heightened anxiety, and reduced stress resilience.
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A naturopath takes a root-cause approach — assessing diet, stress, sleep, microbiome composition, and functional pathology to understand what's driving the imbalance. Tools like GI-MAP stool analysis, microbiome profiling, and comprehensive functional blood panels can reveal specific drivers. Treatment typically includes targeted dietary support, herbal medicine, evidence-based probiotic and prebiotic therapy, and lifestyle interventions aimed at restoring microbiome diversity and reducing neuroinflammation.
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A naturopath doesn't replace a GP or psychologist — and I actively encourage clients to maintain those relationships. What I offer is a different lens: a functional assessment of whether there are physiological drivers — gut dysbiosis, nutritional deficiencies, HPA axis dysregulation, or hormonal imbalances — contributing to mood and anxiety symptoms. In many cases, addressing these physical drivers significantly improves the effectiveness of other mental health support.
Ready to Investigate Your Gut-Brain Health?
As a Microbiome Analyst and Healthy Gut Practitioner trained by Dr Jason Hawrelak at the Microbiome Restoration Center, I work with clients across Australia to assess and support gut health through functional testing, microbiome analysis, and targeted naturopathic treatment.
If you're dealing with mood, energy, or cognitive symptoms alongside gut concerns — or if you've simply never had your gut health properly investigated — this is worth exploring.
References
Irum, N., Afzal, T., Faraz, M. H., Aslam, Z., & Rasheed, F. (2023). The role of gut microbiota in depression: An analysis of the gut-brain axis. Frontiers in Behavioral Neuroscience, 17, Article 1185522. https://doi.org/10.3389/fnbeh.2023.1185522
Kurhaluk, N., Kołodziejska, R., & Kamiński, P. (2025). Integrative neuroimmune role of the parasympathetic nervous system, vagus nerve and gut microbiota in stress modulation: A narrative review. International Journal of Molecular Sciences, 26(23), Article 11706. https://doi.org/10.3390/ijms262311706
Park, J. C., Chang, L., Kwon, H.-K., & Im, S.-H. (2025). Beyond the gut: Decoding the gut–immune–brain axis in health and disease. Cellular & Molecular Immunology, 22(11), 1287–1312. https://doi.org/10.1038/s41423-025-01333-3
