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Does our mental health depend on our gut health?

Updated: Feb 1, 2023

We’ve all felt the feeling of “butterflies in our stomach” and known intuitively that when our mind reads an event as stressful, anxious or exciting, our digestive system reacts. The same phenomenon exists in reverse - we can experience a queasy or “gut feeling” when walking into an uncomfortable or scary situation - which demonstrates that our gut can react faster than our brain. This is the gut and the brain talking to each other. They do so all day, every day via the gut-brain axis which is a bi-directional communication network that links cognitive and emotional centres of the brain to control and function of the gut.

“Your gut mirrors every emotion that arises in your brain”, Emeran Mayer

When we are angry our stomach vigorously contracts, our small intestines twist and spit and we hang onto our food for longer. But when we are stressed or anxious our stomach and intestines rush through the digestion process to rid themselves of food and free up energy for ‘fight or flight’ (our bodies stress response). When we are depressed, our intestines hardly move at all.

How our brain perceives an event can mess up virtually every digestive function we have! But interestingly, most of the communication actually comes from our guts. 90% of the communication signals travel from the gut to the brain via the vagus nerve, which suggests that the brain is highly reliant on information from the gut. Our guts are conveying information about the type of foods we’ve ingested, chemicals that may be present and any pathogens that could have inadvertently entered our body. It also produces hormones which tell our brain whether we are full or hungry (1).

So, with all this communication between the two systems, it makes sense that the there is a high cross over between gastrointestinal disease and psychiatric disorders (2,3). For example, mood disorders affect half of people with Irritable Bowel Syndrome (IBS) (4) and antidepressants are the most common treatment given to these patients (2). Antibiotics are also linked with psychiatric side affects (5). A large population study showed that a single course of antibiotics led to an increased risk for depression and anxiety, rising further the more antibiotics were taken (6).

Whilst this connection between the gut and the brain has been established for some time, we are only just beginning to understand the weird and wonderful world of the microbes that live in our guts. Or in other words, the gut microbiome, and its role in our health.

What is the gut microbiome and what is its role in mental health?

The gut microbiome is a planetary level population of diverse microbes - we have trillions of bacteria, viruses and fungi living in our GI tract. In fact, only 10% of the cells in or on a human being are actually human! (1) So, the question that many scientists are asking today is, who actually governs who? It might be that the microbes are more in control than we have realised - they contain over 7 million genes (1), giving them an incredible capacity to communicate with us and the ability to change our genes depending on our environment and lifestyle. The choices we make day to day can determine how much of our microbiome is made of beneficial vs harmful microbes - when the 'good' and the 'bad' become imbalanced we can experience health issues (9).

Our microbiome shifts as we age - when we are children it is still developing, it reaches its fully formed stage when we are young adults and then drops off again later in life. Scientists have linked this shift in microbiome to age related brain diseases such as childhood autism and those which occur later in life like Parkinson’s and Alzheimer’s (1). These diseases are rapidly rising - autism prevalence has doubled in the last decade, and Parkinson’s and Alzheimer’s are expected to double by 2030 (1). It is interesting that these rises coincide with the increase in lifestyle factors which adversely affect the gut microbiome, such as processed and inflammatory foods, stress and toxin exposure.

It has also been shown that disruptions to the maternal microbiome from things such as infection, poor nutrition or prenatal stress are associated with neurodevelopment disorders including anxiety, Attention Deficit Disorder and depression (10). Whilst the details of how this works requires more research, it does suggest that the health of our mother’s microbiome could be as important as our own, in determining how likely we are to develop mental health disorders.

How does this affect how we think today?

Today, we see mental health disorders as a psychiatric problem. If you are suffering with anxiety or depression, the chances are you’ll be given a drug which tricks your brain into thinking it has more serotonin (our mood regulation hormone) than it does. Your doctor is very unlikely to talk to you about your gut health, despite the fact that 95% of our serotonin is actually produced in the gut.

Psychological stress can, undoubtedly, affect our mental health. Childhood trauma in particular, can lead us to develop a chronically heightened stress response, which puts us at risk of many different issues. Working through unhealthy belief systems with a mental health expert can be a vital part of recovery. But what if psychiatry and psychology are not the only answers? What if we need to look to Gastroenterologists and experts of the gut microbiome to support our healing from mental health disorders?

Through microbiome transplants, scientists have shown that they can make an ‘extrovert mouse’ a ‘timid’ mouse and an obese mouse with a high appetite, a lean mouse with a more moderate appetite (1). The thoughts of the mice were changed by the balance of microbes in their guts. In a human study, women who ate probiotic rich yoghurt (which creates a better microbiome balance) for 4 weeks, had a decreased stress reaction to negative stimuli (1). Through my work in Functional Medicine, I know of hundreds of people who have improved or reversed their anxiety or depression by treating dysfunction in their gut.

"All disease begins in the gut", Hippocrates

This idea, from Hippocrates, is at the foundation of our thinking in Functional Medicine. The wonderful news it that the health of our microbiome is largely dependent on the choices we make around food, sleep and our exposure to stress, so we have the power to change it for the better. Even if we were influenced by our mother’s disrupted microbiome, we can work to improve it with the choices we make today.

Tips for improving the health of your gut microbiome:

1. Create balance

High levels of stress hormones can disrupt the microbiome so take steps to actively manage your stress day to day. Prioritise getting good, deep sleep, move your body frequently and take time to be mindful in and amongst the day's workload.

2. Go plant-based

Plant-based does not mean you can’t eat meat or fish if you want to, it simply means that you get the majority of your nutrition from plants - there is endless evidence to show that this is good for our health. Plants are full of the fibre that our microbiome love to feed on. Diversity is key so try to eat as many different types of plants as you can. Different colours count - so next time you’re buying peppers get the mixed bag! Try delicious, plant based recipes here.

3. Eat fermented foods

Foods such as miso, kefir, kimchi and sauerkraut are rich in probiotics which will re-populate the friendly bacteria in our guts, addressing the balance between the beneficial and harmful microbes. Alternatively, you can take a probiotic supplement. Just remember that not all supplements are made equal - many of the cheaper brands have a low strain count and are filled with unhealthy additives. Pure Encapsulations, Garden of Life and Jarrow are some of the brands I recommend.

4. Root out infections

High levels of stress will suppress the immune system and make it less able to counter pathogens or harmful microbes. As a result, many of us are suffering with simmering infections in the gut such as e-coli, yeast and h-pylori overgrowth. These infections lead to an imbalanced microbiome which creates inflammation in the body, so it’s important to find them and treat them. A good functional medicine practitioner will be able to help you do this.

5. Heal your gut lining

When we have too many harmful microbes in our digestive tract, it can lead to a weakening of the intestine walls and the contents leaking into the bloodstream. This can create inflammation in the body which is linked to the development of brain diseases. A good functional medicine practitioner will be able to help you heal your gut lining if required.

6. Watch your antibiotic use

Antibiotics don’t just kill the harmful bacteria, they kill the good bacteria too. Given that a balance between beneficial and harmful bacteria is what makes a healthy microbiome, antibiotics can often do more harm than good. They can of course be essential when facing a life threatening infection, but for everyday infections you might be better off avoiding them as there is always a price to pay for your long term health. See my blog here about how to strengthen your immune system so you can avoid getting bugs in the first place.


(1)The Mind-Gut Connection, Emeran Mayer, MD

(2) Neufeld KA, Foster JA. Effects of gut microbiota on the brain: implications for psychiatry. J Psychiatry Neurosci 2009; 34: 230–231.

(3) Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Irritable bowel syndrome: a microbiome-gut-brain axis disorder? World J Gastroenterol 2014; 20: 14105–14125.

(4) Whitehead WE, Palsson O, Jones KR. Systematic review of the comorbidity of irritable bowel syndrome with other disorders: what are the causes and implications? Gastroenterology 2002; 122: 1140–1156.

(5) Sternbach H, State R. Antibiotics: neuropsychiatric effects and psychotropic interactions. Harv Rev Psychiatry 1997; 5: 214–226.

(6) Lurie I, Yang YX, Haynes K, Mamtani R, Boursi B. Antibiotic exposure and the risk for depression, anxiety, or psychosis: a nested case-control study. J Clin Psychiatry 2015; 76: 1522–1528.

(7) O'Brien SM, Scott LV, Dinan TG. Cytokines: abnormalities in major depression and implications for pharmacological treatment. Hum Psychopharmacol 2004; 19: 397–403.

(8) Park AJ, Collins J, Blennerhassett PA, Ghia JE, Verdu EF, Bercik P et al. Altered colonic function and microbiota profile in a mouse model of chronic depression. Neurogastroenterol Motil 2013; 25: 733–e575.

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