Stress, the Nervous System & Your Gut

Written By Emily Gibbs

Stress, the Nervous System & Your Gut: The Connection Explained

In recent years, research has revealed just how closely the gut and brain communicate , a two-way relationship often called the gut–brain axis. This connection means that stress doesn’t just affect your mood or sleep — it can directly influence digestion, immunity, and even the types of microbes living in your gut.

When the body is under chronic stress, the nervous system shifts into “fight or flight” mode, diverting energy away from digestion and repair. Over time, this can lead to bloating, changes in appetite, food sensitivities, and altered bowel patterns. Emerging research now shows that these gut changes can, in turn, send distress signals back to the brain , perpetuating a cycle of anxiety, fatigue, and inflammation.

Understanding this connection is transforming how we approach both mental and digestive health, highlighting the importance of addressing the whole system , not just isolated symptoms.

The Gut–Brain Axis: Your Internal Communication Highway

The gut and brain are in constant conversation via the vagus nerve, the body’s main communication line between the central nervous system and the digestive tract. This network transmits signals about mood, hunger, inflammation, and even microbial activity (Cleveland Clinic, 2024).

When functioning optimally, this connection helps regulate digestion, motility, and emotional wellbeing. However, when stress disrupts this pathway, it can alter how the gut moves, how nutrients are absorbed, and how microbes behave , often leading to symptoms like bloating, reflux, constipation, or loose stools.

Recent evidence highlights that the bidirectional microbiota–gut–brain axis links stress to depression and other mood disturbances, with the microbiota itself influencing neural circuits that regulate stress and emotion (Mayer et al., 2023).

The Role of the Nervous System in Digestion

Your autonomic nervous system has two main branches:

  • Sympathetic (Fight or Flight): Activated during stress, prioritising survival over digestion.

  • Parasympathetic (Rest and Digest): Responsible for relaxation, optimal enzyme secretion, and healthy gut movement.

When stress is ongoing, the sympathetic system dominates. This means less stomach acid and digestive enzyme production, reduced gut motility, and compromised nutrient absorption. Over time, this can contribute to gut inflammation, dysbiosis, and symptoms such as IBS, nausea, or food sensitivities.

Physiological research shows that both acute and chronic stress can alter gastrointestinal parameters including motility, mucosal integrity, and secretion (Konturek et al., 2021).

How Stress Impacts Your Gut Microbiome

Chronic stress doesn’t just alter hormones — it reshapes your gut ecosystem. Stress hormones such as cortisol and adrenaline have been shown to:

  • Reduce beneficial bacteria such as Lactobacillus and Bifidobacterium (Xu et al., 2019)

  • Increase inflammatory species linked to fatigue, mood changes, and metabolic dysfunction (Tseng et al., 2020)

  • Weaken the gut barrier (“leaky gut”), allowing toxins and inflammatory molecules to enter circulation (Mu et al., 2020)

Even short-term stress can impact intestinal permeability. A controlled study found that laboratory stress increased gut permeability in individuals with elevated cortisol (Vanuytsel et al., 2014).

Further evidence confirms that stress hormones directly interact with the gut microbiota, influencing inflammation and behavioural outcomes — creating a loop that links stress, microbiome changes, and mental health (Gao et al., 2024).

Signs Your Gut & Nervous System Are Out of Balance

You may notice symptoms that span both the mind and body:

  • Frequent bloating or irregular bowels — heightened stress can alter gut motility and enzyme secretion, leading to constipation, diarrhoea, or alternating patterns.

  • Anxiety or feeling “on edge” — over 90% of serotonin is produced in the gut; dysbiosis or inflammation can impact neurotransmitter balance, affecting mood and emotional regulation.

  • Poor appetite or sugar cravings — fluctuations in cortisol and gut bacteria can alter hunger hormones (ghrelin and leptin), increasing cravings for quick-energy foods.

  • Sleep disturbances — gut inflammation and stress hormones interfere with melatonin synthesis, disrupting circadian rhythm and deep sleep cycles.

  • Fatigue and brain fog — inflammation in the gut can trigger systemic effects, impairing mitochondrial energy production and cognitive clarity (Simpson et al., 2021).

  • Food sensitivities or skin flare-ups — stress and microbial imbalance can weaken the gut barrier (“leaky gut”), allowing antigens to trigger immune or inflammatory skin responses (Mu et al., 2020).

These symptoms are your body’s way of signalling that it’s time to slow down and restore balance.

Naturopathic Approaches to Restore the Gut–Brain Connection

A holistic, functional approach aims to support both the nervous system and the gut simultaneously. At EMME Naturopathy, this often includes:

1. Nervous System Regulation
Herbal medicine and nutrients such as Withania somnifera, Passiflora incarnata, magnesium, and B-vitamins help modulate cortisol and improve resilience to stress (Lopresti et al., 2019).

2. Gut Repair & Microbiome Support
Tailored probiotics, prebiotics, and gut-healing nutrients (such as L-glutamine, zinc carnosine, and omega-3 fatty acids) support microbial diversity and strengthen the gut barrier.

3. Functional Testing
Advanced testing such as the Microbiome Mapping Stool Testing or Organic Acids Test (OAT) can identify microbial imbalances, inflammation, and nutrient deficiencies that may contribute to both gut and mood symptoms.

4. Lifestyle & Mind–Body Practices
Breath work, gut-directed hypnotherapy, mindful eating, yoga, time in nature, and adequate sleep all help shift the body back into a parasympathetic “rest and digest” state.

Rebalancing for Long-Term Health

Healing the gut–brain connection is about creating space for balance, nourishment, and calm. By supporting the nervous system and restoring microbial diversity, you can improve not only digestion, but also energy, mood, and resilience to stress.

Ready to Support Your Gut–Brain Connection?

If you’re experiencing ongoing stress, fatigue, or digestive symptoms, a naturopathic consultation can help uncover the root cause and design a personalised plan to restore balance.

Click Here to book an appointment or connect with us for a free discovery call.

References

Cleveland Clinic. (2024). The gut-brain connection. Cleveland Clinic. https://my.clevelandclinic.org/health/body/the-gut-brain-connection

Gao, X., et al. (2024). Stress-induced anxiety and depressive-like behaviours correlate with dysbiosis of gut microbiota. Frontiers in Molecular Neuroscience, 17, 1415567. https://doi.org/10.3389/fnmol.2024.1415567

Konturek, P. C., Brzozowski, T., & Konturek, S. J. (2021). Stress and the gut: Pathophysiology, clinical consequences, diagnostic approach and treatment options. The Journal of Physiology, 599(18), 4315–4331. https://doi.org/10.1113/JP281951

Lopresti, A. L., Drummond, P. D., & Smith, S. J. (2019). A review of clinical trials examining the anxiolytic effects of Withania somnifera (ashwagandha). Phytotherapy Research, 33(3), 865–876. https://doi.org/10.1002/ptr.6274

Mayer, E. A., Tillisch, K., & Gupta, A. (2023). The microbiota–gut–brain axis: From basic neuroscience to clinical relevance. Frontiers in Neuroscience, 17, 1151478. https://doi.org/10.3389/fnins.2023.1151478

Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2020). The gut microbiota and autoimmune diseases: A two-way street. Clinical Reviews in Allergy & Immunology, 58(1), 90–107. https://doi.org/10.1007/s12016-019-08736-8

Simpson, C. A., Diaz-Arteche, C., Eliby, D., Schwartz, O. S., Simmons, J. G., & Cowan, C. S. M. (2021). The human gut microbiota and stress resilience: A review of the microbiota-gut-brain axis. Microorganisms, 9(4), 723. https://doi.org/10.3390/microorganisms9040723

Tseng, C. H., Wu, C. Y., & Lin, J. T. (2020). Gut microbiota dysbiosis and cortisol-degrading bacteria in Cushing’s syndrome. The Journal of Clinical Endocrinology & Metabolism, 105(12), dgaa572. https://doi.org/10.1210/clinem/dgaa572

Vanuytsel, T., Van Wanrooy, S., Vanheel, H., Vanormelingen, C., Verschueren, S., Houben, E., Salim, R., Törnblom, H., Simrén, M., & Tack, J. (2014). Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans. Gut, 63(8), 1293–1299. https://doi.org/10.1136/gutjnl-2013-305690

Xu, Y., Wang, N., Tan, H. Y., Li, S., Zhang, C., Zhang, Z., & Feng, Y. (2019). Chronic stress-induced gut microbiota dysbiosis and visceral hypersensitivity. Frontiers in Microbiology, 10, 3067. https://doi.org/10.3389/fmicb.2019.03067

Emily Gibbs
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