Why the Gut Microbiome is crucial for your Mental Health

The Diet-Whisperer
11 min readJun 10, 2021


Gut Bugs: What are they?

Bugs are small organisms made up of single cells, and they have been around a lot longer that humans. They were the earliest forms of life, and first developed over three billion years ago. You live with trillions of bugs in your guts. Your gut bugs outnumber your own cells, weighing in heavier than your brain!

At the diet-whisperer we love gut bugs and you can find out a lot more them in our whisperer blog. Gut bugs beat you on many fronts: genes win prizes, genes are the controllers and instigators of manufacturing and you have a measly 30,000 genes; your gut bugs beat you two hundred-fold with millions of genes. Not just that, you are outnumbered by your gut bugs. You have 31 trillion human cells, (unless you are an alien) and your gut bugs number at least 38 trillion cells, but possibly more.

With this vast number of cells and genetic power, your gut bugs have powers to exert a major effect on you, their hosts. They have more influence over you than you imagine!

Who speaks to your Brain? That’ll be your gut and gut bugs

Your gut constantly speaks to your brain. You feel a bit low; you have a biscuit and voila, an instant smile, you feel great: a fluttering feeling in your stomach when you are just about to get on stage? That’s your gut and brain working together.

In medical school, back in the 80s, conventional wisdom was that the vagus or wandering nerve served the brain, relaying messages to the gut; it was a one-way system, the brain very much being the master. But it is now known, that is not the case; the vagus nerve is very much a two-way system, and the gut both sends and receives messages to your brain via this information highway.

Not just does your gut communicate with your brain, so do your gut bugs. Gut bugs secrete chemicals directly into the blood, which are then taken to the brain. Gut bugs excite tissues in the gut lining that stimulate the vagus nerve and they activate hormone producing cells in the gut lining, which affect your brain. They have a very important role to play in the immune system, which indirectly affects your brain.

This communication system is called the Microbiome-Gut-Brain Axis. As with any effective communication system, continuous rapport allows gut bugs to exert a major influence on your brain.1

What do gut Bugs do?

Your gut bugs provide you with thousands of essential chemicals; chemicals, which you can’t make, and on which your life depends. Humans have evolved with gut bugs for millions of years. In turn, you need to provide gut bugs with their food, water, and shelter.

Many of the chemicals produced by gut bugs act on your brain and nervous system, so-called neuroactive chemicals or neurotransmitters. These include serotonin, dopamine, adrenaline, tryptamine and short chain fatty acids. The process of production of these chemicals is complicated and needs coordination of your gut, brain and gut bugs.

Serotonin gives you a mood boost. You probably know about serotonin because Prozac, a so-called ‘Happy pill’ works by increasing serotonin levels. In simple terms, too little serotonin, and you are depressed; conversely the right level of serotonin and your mood is good. Healthy gut bugs play a key role in maintaining the right level of serotonin and this means that you feel good.

How bugs affect your mood

Gut bugs change your mood by the production of neuroactive chemicals, which are then absorbed into the circulation. Cryan et al were amongst the first group to show that gut bugs influence our emotions. 2 They introduced the concept of the psychobiome; these are the gut bugs that alter how you think, feel and act. They showed that your gut bugs can affect your brain function. What happened to free will? They also showed that people who are depressed have a different composition of gut bugs than people who are not depressed. And we know that serotonin is responsible for our mood and is produced in the gut, with the aid of your gut bugs.

Short chain fatty acids are among the many neuroactive chemicals produced by gut bugs. These short chain fatty acids have many effects including affecting our mood; gamma-aminobutyric acid helps to control feelings of fear and anxiety and propionate is involved in satiety.

How can it go wrong?

When you are in harmony with your gut bugs; your body is a temple, poetry in motion: you feel great, you look young, and you move easily. But it can all go horribly wrong, with disastrous consequences for your health.

There is an established association between brain disease and bowel symptoms, recognised for millennia; Plato said, “All diseases begin in the gut”. Parkinson’s disease is associated with constipation, and constipation can be the first sign of the illness. Irritable bowel syndrome is associated with psychological symptoms, depression associated with digestive symptoms and the list goes on. Gut bugs have now entered the fray.

The discovery that inflammation plays a role in the development of brain diseases, led to the concept that diet plays a role in mental health, and this association involves the role of gut bugs. 3 Changes in gut bugs have been identified in autism, schizophrenia, and attention deficit disorder, as well as mood disorders such as depression, anxiety, and stress. Both Alzheimer’s disease and Parkinson’s disease have been linked to gut bug changes. Children with autism often have abnormal and fewer species in their gut bugs.

In the Flemish Gut Flora Project, the presence of butyrate producing bugs were consistently associated with a higher quality of life. Depletion of butyrate producing bugs was associated with depression. 4

We all suffer stress, but some people become anxious, and others do not. We tend to admire people who show this characteristic, but maybe we should admire their gut bugs instead? Bear et al performed a metanalysis of studies, which looked at the relationship of stress resilience to gut bug composition.5 Stress resilience is the ability to withstand stress without developing anxiety, depression, or mood disorders; a characteristic badly needed in these COVID times. While many factors influence your response to stress, gut bugs are emerging as a significant player. Supporting good gut bugs is likely to confer increased stress resilience.

The relationship between sick gut bugs, also called dysbiosis and mental disease is building, and the topic is still one that requires further work, within which there is conflicting evidence. But there is increasing evidence that characteristic gut bugs changes are related to mental disorders. Whether the gut bugs changes are the cause or effect remains to be confirmed. 2

Does helping gut bugs help mental disease?

Medications used for mental diseases do not work in all patients and these tablets frequently have unpleasant side effects. This has led to the search for new safe, effective treatments. Gut bug based treatment for mental health is a new exciting field, with huge promise. The terms nutritional psychiatry or psychobiotics refers to the direct treatment of gut bugs in the management of mental disease. Medics are talking excitedly about a psychobiotic revolution. 6

The treatment of gut bugs involves either the use of prebiotics and/or probiotics. Prebiotic mean a change in diet with high fiber food or supplements. Probiotics contain live bacteria and can be in the form of food, or the bugs can be freeze-dried and administered in tablet form. Many studies have reported successes with such approaches to treatment.

Yang et al, in a metanalysis reviewed the role of gut bug treatment in the management of anxiety. 7 Anxiety may affect as many as a third of people in their lifetime. They report that 11 of 21 studies confirm the positive effects of treatment of gut bugs for anxiety. The studies where dietary adjustment, or prebiotics was the main approach were more successful than the studies using probiotic supplements.

Probiotics have been associated with positive outcomes in several trials evaluating the effect on mood. A probiotic mix treatment had a positive effect on mood in a study of healthy female volunteers. 8 A healthy elderly population reported a positive effect on mood following probiotic treatment for three weeks with live yoghurt. 9 A probiotic reduced exam stress levels in healthy students, after only two weeks of treatment. 10

A healthy diet supports gut bugs and thus serotonin production. A study in Spain evaluating over 40,00 people showed that people who are not depressed have a healthier diet than people who are depressed. 11 Similar findings in Canada in 25,000 people revealed that a healthy diet over the course of one year was associated with fewer physician visits for depression. As the diet score improved, there were even fewer visits for depression. 12

How do I support my Gut Bugs?

You can improve your gut bugs; you can help your gut bugs and it will make a difference to your life. Gut bugs respond to a change in diet and the improvements can happen very rapidly. Gut bugs feed on fiber and the key to helping your gut bugs is to eat fiber-a lot of fiber. Fiber is found in vegetables, particularly green vegetables.

Smoothies do not have fiber, processed food is almost totally without fiber and should be avoided-that is the super-refined carbs-sweets, biscuits, muffins, cakes etc. If you eat processed food, you encourage the bad bugs which then outnumber the good bugs and you are in a downward spiral of poor health.

Probiotics in food will help; live yoghurt, live cheeses (banned in USA!!!!), kefir, kombucha and fermented vegetables are good examples. A healthy lifestyle with adequate sleep, exercise and stress reduction helps to support a good gut bug colony.

What about antibiotics?

The misuse and abuse of antibiotics has heralded a modern health scare; resistance to antibiotics, and this problem is constantly in the news. But far more worrying to us here in Whisperer HQ, is the adverse effect that antibiotics have on gut bugs, in both humans and animals. Commercialisation of farming heralded the ubiquitous use of antibiotics in animal food, and the animals retain antibiotic residue, which we then consume. This can have adverse effects even in the tiny doses eaten. 1 Worrying, isn’t it?

Antibiotics kill bugs including gut bugs. Just think, you work hard for years cultivating your gut bugs and one course of misjudged antibiotics ruins all your efforts. It can take 6–9 months to restore a healthy gut bug colony, following a course of antibiotics. Sometimes the gut bug colony never reverts to normal, even after a single course of antibiotics. And researchers have confirmed an increase in depression in people taking antibiotics.

We have some advice on antibiotics: Use antibiotics only in serious or life-threatening illnesses. AVOID ANTIBIOTICS IF YOU CAN.

And Now?

Don’t expect to go to your doctor and be given advice about your gut bugs if you have mental problems. It will take many years before this type of treatment has gone through the necessary, rigorous testing. But regardless of whether you are seeking better mental health or keen to look after yourself; there is no downside to looking after your gut bugs and no safety issues on looking after your gut bugs. So, why not start today and think about the 38 trillion cells in your gut, influencing your mental health and well-being in so many ways? You will never regret tending your gut bug allotment. If you enjoyed this article, we have books and a free monthly newsletter on diet and fitness to learn much more about your gut and how it relates to your health.


Gut bugs are intimately connected with your brain. In health, your gut bugs provide you with essential chemicals, but gut bugs need to be looked after and need the right food. Fiber is the key ingredient, and it is known that most people do not eat enough fiber. Deterioration of the gut bug colony is associated with mental health disease, including mood disorders. Research, whilst in its infancy is looking at treating mental health disorders by treating gut bugs and this is showing promise.

Aren’t you amazed that humans, as intelligent as we consider ourselves to be, are partially controlled by bugs-single cell organisms!

Blog Whisperings

  • Gut bugs are critical for health-both mental and physical
  • Gut bugs have an effective communication system with the brain
  • Gut bugs produce chemicals which influence the brain
  • Gut bugs are involved in the production of the mood-altering hormone serotonin
  • Mental disease is associated with abnormalities of gut bugs
  • Avoid antibiotics, unless absolutely necessary
  • Psychobiotics or nutritional psychiatry is the treatment of mental problems by directly targeting gut bugs
  • To support gut bugs-eat fiber, eat lots of fiber
  • Probiotics such as kefir, kombucha, fermented vegetables, live yoghurt and cheeses support healthy gut bugs
  • Supporting a healthy gut bug colony helps with mental health
  • Gut bugs can be altered, supported, and improved by a healthy diet and lifestyle
  • Nurture your gut bugs to reap health rewards


1. Karakan T, Ozkul C, Küpeli Akkol E, Bilici S, Sobarzo-Sánchez E, Capasso R. Gut-Brain-Microbiota Axis: Antibiotics and Functional Gastrointestinal Disorders. Nutrients. 2021 Jan 27;13(2):389. https://pubmed.ncbi.nlm.nih.gov/33513791/

2. Margolis KG, Cryan JF, Mayer EA. The Microbiota-Gut-Brain Axis: From Motility to Mood. Gastroenterology. 2021 Apr;160(5):1486–1501. https://pubmed.ncbi.nlm.nih.gov/33493503/

3. Grosso G. Nutritional Psychiatry: How Diet Affects Brain through Gut Microbiota. Nutrients. 2021 Apr 14;13(4):1282. https://pubmed.ncbi.nlm.nih.gov/33919680/

4. Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol. 2019 Apr;4(4):623–632. https://pubmed.ncbi.nlm.nih.gov/30718848/

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6. Long-Smith C, O’Riordan KJ, Clarke G, Stanton C, Dinan TG, Cryan JF. Microbiota-Gut-Brain Axis: New Therapeutic Opportunities. Annu Rev Pharmacol Toxicol. 2020 Jan 6;60:477–502.

7. Yang B, Wei J, Ju P,
et al. Effects of regulating intestinal microbiota on anxiety symptoms: A systematic review. General Psychiatry 2019;32:e100056. https://pubmed.ncbi.nlm.nih.gov/31179435/

8. Bagga D, Aigner CS, Reichert JL, Cecchetto C, Fischmeister FPS, Holzer P, Moissl-Eichinger C, Schöpf V. Influence of 4-week multi-strain probiotic administration on resting-state functional connectivity in healthy volunteers. Eur J Nutr. 2019 Aug;58(5):1821–1827. https://pubmed.ncbi.nlm.nih.gov/29850990/

9. Benton D, Williams C, Brown A. Impact of consuming a milk drink containing a probiotic on mood and cognition. Eur J Clin Nutr. 2007 Mar;61(3):355–61. https://pubmed.ncbi.nlm.nih.gov/17151594/

10. Andersson H, Tullberg C, Ahrné S, Hamberg K, Lazou Ahrén I, Molin G, Sonesson M, Håkansson Å. Oral Administration of Lactobacillus plantarum 299v Reduces Cortisol Levels in Human Saliva during Examination Induced Stress: A Randomized, Double-Blind Controlled Trial. Int J Microbiol. 2016;2016:8469018. https://pubmed.ncbi.nlm.nih.gov/28101105/

11. Cebrino J, Portero de la Cruz S. Diet Quality and Sociodemographic, Lifestyle, and Health-Related Determinants among People with Depression in Spain: New Evidence from a Cross-Sectional Population-Based Study (2011–2017). Nutrients. 2020 Dec 30;13(1):106. https://pubmed.ncbi.nlm.nih.gov/33396825/

12. Marozoff S, Veugelers PJ, Dabravolskaj J, Eurich DT, Ye M, Maximova K. Diet Quality and Health Service Utilization for Depression: A Prospective Investigation of Adults in Alberta’s Tomorrow Project. Nutrients. 2020 Aug 13;12(8):2437. https://pubmed.ncbi.nlm.nih.gov/32823652/



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