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The Impact Of Stress On The Gut Microbiome

The Impact Of Stress On The Gut Microbiome

Could stress be harming your gut health? How not taking time to unwind could hinder your gut healing efforts. 

Have you ever experienced butterflies or an upset stomach due to nerves, worry or anxiety? Then you’ve experienced the powerful connection of the gut-brain axis.  

Due to world and local current affairs we’re all feeling stressed – to put it mildly. So, what does the gut-brain connection mean for the chronically stressed among us? We’re living in a time where the word ‘unprecedented’ comes up a lot. This unfortunately has also meant unprecedented impacts on our health – particularly the nervous system and the gut.

The impact of COVID-19 on the gut and mental health

COVID-19 has been devastating in every conceivable way. While all major, sudden change and tragedy comes with the opportunity for renewal, growth and fresh perspectives, it’s important not to glaze over the very real effects that such sustained stress has had on our lives, our bodies and of course, our microbiomes.

Unsurprisingly, spikes in depression, anxiety and stress during these times have been associated with major changes to our daily habits around health – a survey from April 2020 of 1,491 Australian adults revealed that as a nation we’re exercising less, experiencing poor sleep quality, and tobacco and alcohol sales have increased.1 Sadly, all of these changes have a huge influence on all areas of health, but especially gut, general immunity and mental health.

Stress prevents the activity of the vagus nerve and reduces vagal tone. This in turn can cause damage to the gastrointestinal tract, which is intrinsically connected to the vagus nerve. The composition of the gut microbiome is also damaged by these impacts to the vagus nerve. Perhaps the effects of this will be another thing that will be ‘unprecedented’ in the months and years to come.

The gut-brain axis

The brain and the gut are constantly communicating via the gut-brain axis. The gut-brain axis encompasses the central nervous system (CNS), which also includes the spinal cord and nerves branching off it, as well as the digestive system.

In recent years, the gut bacteria has been uncovered as one of the main regulators of the connection and function between the gut-brain axis. In fact, much like a gossiping neighbour, the bacteria of the microbiome are in constant contact, telling the brain all about what’s going on in all other body systems. The ‘telephone lines’ for this communication include the vagus nerve and enteric nervous system (the part of the nervous system that runs through the gut), the immune system and various metabolic pathways.2

How stress affects gut bacteria

Mental health conditions like stress, anxiety and depression reshape the composition of the gut microbiome. The ideal microbiome composition is one brimming with beneficial bacteria species like Lactobacillus and Bifidobacterium that aid with digestion, including the break down and absorption of nutrients, support the immune system and even reduce symptoms of anxiety and depression.3

An increase in stress hormones such as cortisol increase inflammation and reshape the composition of the gut bacteria in the microbiome.2 The gut bacteria are strongly influenced by elevated stress hormones, inflammation, as well as changes to the autonomic nervous system that controls processes like heart rate, blood pressure and digestion.4

Heightened stress can trigger a boost to the populations of harmful bacteria that are known to encourage dysbiosis and leaky gut syndrome. Cortisol and inflammatory cells that are released during a stressful event can also weaken the gut barrier even further.4

How stress and the microbiome change our food choices

We know that what we eat strongly influences the types of bacteria that are able to thrive in the microbiome. So, what happens when a period of stress isn’t well managed? It’s human nature to look to comfort foods to self-soothe in difficult times – but those comfort foods have radically changed since the days of Nana’s chicken soup or homemade biscuits.

As so many of us now feel time-poor and less capable of making good decisions, we find ourselves reaching for convenience foods – packaged, processed, high in adulterated fat, refined sugar and salt – essentially all of the things that harmful bacteria thrive on. This becomes a feedback system where, as the population of toxic species like Clostridium, Staphylococcus, and Escherichia coli grow, they begin to influence our cravings. This occurs because these harmful gut bacteria actually produce molecules that look just like hormones the body naturally produces to regulate appetite.4 Once they’re in the driver’s seat, these bacteria can have us craving junk food in a way that feels almost out of our control.

These sneaky bacteria can influence taste receptors, and release feel good ‘reward’ chemicals like serotonin and dopamine – leading to behavioural and mood changes. In fact, some bacterial species can even influence dysregulated eating behaviours like bingeing or restriction.4

So, while you may be ready to move past a stressful time in your life, the microbiome can actually keep you stuck in old patterns.

Stress, the microbiome and digestive disease

Chronic stress and nervous system activation is related to inflammation, including of the gut. Inflammation in the gut, as we now know, drives poor digestion and absorption, digestive complaints like constipation, diarrhoea, indigestion, stomach cramps, leaky gut syndrome and even food allergies. If ignored, these symptoms of digestive distress can lead to more serious conditions.

Autoimmune disease is a classification of disease whereby the immune system mistakes the body’s own healthy cells for foreign invaders and attacks them. Autoimmune diseases are on the rise – around 3-9% per year, depending on the specific condition. Some of the most common autoimmune diseases include rheumatoid arthritis, IBD, type 1 diabetes, multiple sclerosis and Coeliac disease (this has had the greatest increase of 4-9% per year).5

What does this have to do with increases in stress and the gut microbiome? We know now that the intestinal bacteria change in response to stress. Researchers have discovered that these changes to bacteria stimulate activity of immune cells in such a way that they begin to attack the body’s cells and tissues, leading to autoimmune disease.6

Inflammatory bowel disease (IBD) is an autoimmune disease of the digestive tract and includes Crohn’s disease (diagnosed by inflammation of the digestive tract lining), and ulcerative colitis (diagnosed by presence of inflammation deep into layers of the lining of the digestive tract, as well as ulcers).7 Major changes to the gut microbiome is a significant factor in the development of IBD – and reinstating balance through pre- and probiotics is one of the most important aspects of treatment for IBD patients.8 Poor vagal tone is also found in IBD sufferers and this, as we now know, can also lead to changes in the gut microbiome.9,10

How to heal the gut-brain axis

The whole idea of an ‘axis’ is that it can run in both directions. So, when we’re looking at how to heal the gut-brain axis it’s essential that both areas are well covered.

All treatment protocols for healing the gut-brain axis will have an element of correcting dysbiosis, re-seeding the gut, healing and reducing inflammation, as well as supporting and toning the nervous system. We don’t just want to feel better for now, we’re aiming for long-term great gut health and a strong, flexible nervous system. After all, there will always be triggers, times of grief and times of even being busy but happy. Tending to the nervous and digestive systems on a daily basis is an insurance policy for unexpected change and stress in the future.

Here are some of my favourite daily habits for supporting the health of the gut microbiome, the digestion and nervous system:

  • Reduce stress in small ways every day, such as turning off the news and going for an evening walk instead and watching the sunset (this also helps to restore circadian rhythm). Place a few drops of your favourite, calming aromatherapy oil in a diffuser, get an early night, de-clutter your space, find a meditation app that works for you and set a reminder for 10 minutes every day. If you’re struggling or have major life stress, book a time with a psychologist, psychotherapist, counsellor or hypnotherapist who resonates with you.
  • Yoga poses, massage, deep breathing, singing, eating healthy fats – they all feel great and they all help to tone the vagus nerve.
  • Move your body. Exercise is not only one of the best possible ways to de-stress and improve your mood, it also supports a healthy gut microbiome.
  • Include plenty of probiotic and prebiotic food sources in your diet to support those beneficial bacteria. As we now know, probiotics also influence healthier food choices, reduce anxiety, inflammation, and prevent autoimmunity, all while boosting the immune system.
  • Avoid inflammation-causing foods and beverages like processed, packaged snack foods, vegetable oil-laden takeaways and alcohol. Focus on an anti-inflammatory diet packed with colourful vegetables, grass-fed animal protein, wild-caught fish, pasture-raised eggs, antioxidant-rich herbs and spices, nuts and seeds, fats from butter, ghee, olive oil, flaxseed and hempseed oil.
  • Drink plenty of filtered water and herbal teas to help support digestive function. The best teas for the gut include ginger, cinnamon, turmeric, peppermint, chamomile, fennel, slippery elm, marshmallow root and dandelion root. Even black tea varieties like English breakfast and earl grey support digestive health.11
  • Practice self or co-regulation at mealtimes. The physiology of stress draws energy away from digestion and can cause damage over time. If dinner time in your house is a stressful time (i.e. you have young children or you’re eating in front of your computer screen) practicing self-/co-regulation can be powerful. We can do this by showing care and affection and by providing a structured, secure and calm environment for mealtimes (and really all the time!). It’s also the perfect time to pay attention to feelings, thoughts, beliefs and behaviours that can creep up on us and spend some time unpacking those either on your own or as a family.12 Whether you live alone or have a bustling household, mealtime is the perfect time for mindfulness and connection.

The emerging research around the gut-brain axis and the powerful impacts of the microbiome is complex and can feel overwhelming. Yet, so often in health it all comes back down to simple, daily practices. Our world is going through a period of unprecedented trauma. As a collective we feel and deal with this information daily - now our bodies and microbiomes are showing the effects of this. While we can’t change what’s happening around us, we have the power every day to decide to alter our inner world – and the effects of that have the potential to be profound to our outer world too.


  1. Stanton, R., Quyen, G.T., Khalesi, S., Williams, S.L., Alley, S.J., et al. Depression, Anxiety and Stress during COVID-19: Associations with Changes to Physical Activity, Sleep, Tobacco and Alcohol Use in Australian Adults. J. Environ. Res. Public Health, 2020;17(11):4065.
  2. Cryan, J.G., O’Riordan, K.J., Cowan, C.S.M., Sandhu, K.V., Bastiaanssen, T.F.S., et al. The Microbiota-Gut-Brain Axis. Physiological Reviews, 2019;99(4):1877-2013.
  3. Can Probiotics Help With Depression? Written March 2019, accessed September 2021 from
  4. Madison, A. & Kiecolt-Glaser, J.K. Stress, depression, diet, and the gut microbiota: human-bacteria interactions at the core of psychoneuroimmunology and nutrition. Curr Opin Behav Sci, 2019;28:105-110.
  5. British Society for Immunology. Are you #Autoimmune Aware? Report for parliamentarians into autoimmune conditions, 2018. Accessed September 2021 from
  6. Werbner, M., Barsheshet, Y., Werbner, N., Zigdon, M., Averbuch, I., et al. Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells. ASM Jounals, 2019,4(4).
  7. Mayo Clinic. Inflammatory bowel disease (IBD). Updated November 2020, accessed September 2021 from
  8. Khan, I., Ullah, N., Zha, L., Bai, Y., Khan, A., et al. Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause of Consequence? IBD Treatment Targeting the Gut Microbiome. Pathogens, 2019;8(3):126.
  9. Bonaz, B., Sinniger, V. & Pellissier, S. Therapeutic Potential of Vagus Nerve Stimulation for Inflammatory Bowel Diseases. Front Neurosci, 2021;15:650971.
  10. Breit, S., Kupferberg, A., Rogler, G. & Hasler, G. Vagus Nerve as Modulator of the Brain-Gut Axis in Psychiatric and Inflammatory Disorders. Psychiatry, 2018.
  11. 9 Teas That Can Improve Digestion, 2019. Accessed September 2021 from
  12. Columbia University Irving Medical Center. The Unsung Benefits of Mealtime with Your Family. Written May 2021, accessed September 2021 from