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Gut-Brain Connection #2 - Fix your gut to fix your brain.

Updated: Oct 21, 2021

In previous article, I have introduced the gut-brain axis, the bidirectional communication alley between your brain and your entire digestive system including microbiome. We talked about how this communication is established, what are some key players & mediators that relay different information and we briefly discussed how things can go wrong.

In this part, I will aim to give you practical, real-life examples of what you can do to:

  • Avoid harming your brain by not harming your gut

  • Support your microbial diversity and integrity

  • To support both your intestinal barrier & blood-brain barrier as both are key mediators of this communication



Alcohol is one of the greatest disruptors of gut health. When consumed, it enters the intestines and starts disrupting the integrity of the intestinal wall causing a state called “increased intestinal permeability”, a situation that can cause serious health problems including severe autoimmune diseases. Alcohol kills good bacteria in our gut; it greatly harms the balance and the density of good bacteria and promotes the growth of “bad” pathogenic bacteria. Although it does not reach the colon (area of greatest microbial density) before being absorbed, it can significantly distort the microbiome in small intestine and induce a state called SIBO (small-intestinal bacterial overgrowth) an extremely difficult digestive condition to get rid. Not only that but these pathogenic bacteria may then start metabolising the alcohol into aldehyde (this should only happen in the liver, the gut cannot deal with aldehyde), which can cause significant toxicity and inflammation in the digestive system. Aldehyde in the gut damages DNS of the cells inside the intestines, and this can lead to the development of carcinogenic cells.

Alcohol as a carcinogen increases the risk of cancers throughout the whole body, including pancreatic cancer, the most severe and the most difficult to cure of all cancers. As such, alcohol has no place in a healthy lifestyle, and the times when it is used should be reserved to the rarest of celebrations and personal achievements rather than being a regular weekly (or daily) habit.


At the level of the microbiome, it appears smoking is not a significant disruptor; however, it impacts other areas of the gut-brain connection. Smoking increases something called “oxidative damage” which is damage caused by aggressive waste products called free radicals. This may damage the walls of the intestines and cause loss of integrity (mentioned previously and in part 1). At the same time, we know that smoking causes a build-up of a variety of toxins.

One of these are Polycyclic Aromatic Hydrocarbons (PAHs), known carcinogens, disruptors of the blood-brain barrier and a contributing factor to dementia. Other toxins coming from smoking are benzene, arsenic, cadmium, nickel, 2-naphtyl-amine, 4-aminobiphenyl and many others. Tobacco leaf is also exposed to many pesticides and insecticides when grown which may get inhaled as the plant is combusted. Many of these are significant carcinogens and brain disruptors.

Vaping is less destructive, and people coming of tobacco towards e-cigarettes have improved blood pressure and reduced markers of inflammation; e-cigarettes commonly expose users to chemicals such as acetaldehyde, formaldehyde, nitrates and other cell-damaging compounds. Ideally, e-cigs should be a transition from smoking to non-smoking, but they should not become the end-point.


Antibiotics are one of the greatest discoveries in modern medicine for fighting severe, potentially lethal infections and they have saved millions of lives since their discovery, especially in times of war and post-war injuries. However, what we see today is a great deal of over-prescription and prescribing antibiotics without proper examination or diagnosis. On top of that, we see the occurrence of something called “superbugs”, pathogenic bacteria that is completely resistant to all known antibiotics. This has tipped the balance of benefit and caused many potential downsides, including significant disruption to the microbiome balance.

Besides AB, many other drugs have been found to damage microbiome and the intestinal integrity. The takeaway here is don’t take any drugs unless you have to. Don’t swallow unnecessary painkillers, don’t use paracetamol to fight a hangover, don’t abuse performance-enhancing drugs etc. Of course, if antibiotics or drugs are prescribed for a chronic condition, you have to take them.

Picture1: Antibiotic-induced disruption to the gut-brain axis in mice.

Source: Hao, W. et al. (2020), 'A review of antibiotics, depression and the gut microbiome', Psychiatry Research PMC 31791704


Consuming an imbalanced diet high in sugar, salt, animal protein & animal fat with a lack of fruits, vegetables, fibre, and natural plant polyphenols (beneficial chemicals in plants) have been shown to have detrimental effects on the general composition of the microbiome. Excess consumption of salt, for example, increases inflammation in the body, which then has a knock-off effect on everything else. Lack of fibre leads to reduced production of Short-Chain Fatty Acids (see part 1), which might have negative effects on BDNF (see article on BDNF)


Consuming protein in the diet is essential as protein is not only a major building block of muscles but also in a variety of neurotransmitters, enzymes, signal proteins, and so sufficient intake of protein is necessary for optimal health. Excess protein, however, especially excess animal protein, has been associated with disruptions of the microbiome. Many major colonies of beneficial bacteria are being reduced by high meat consumption. Very high protein doses while eating low fibre may cause some of the proteins to putrefy in the colon and cause a production of toxic waste molecules like cadaverine that (as the name says) can have negative consequences for health. Excess beef consumption also stimulates the production of a compound called TMAO, which has been associated with colorectal cancer and serious disease, including disruptions to the blood-brain barrier.

Picture 2: The effect of animal and plant protein of specific bacterial species.

Source: Singh, R.K. et al. (2017). 'Influence of diet on the gut microbiome

and implications for human health', Journal of Translational Medicine


It appears that fat in the diet does not have as significant an impact on the gut microbiome; however, we know that diets high in saturated fats (mostly from meat & eggs) increase markers of inflammation in the body which will then have a negative effect on mental health and cognitive performance. Ideally, fat in the diet should come mostly from plants (nuts, seeds, avocados) and some animal products (e.g. small oily fish, some eggs, a little bit of dairy); however, the latter is not required in a healthy diet.


Of the three macronutrients, carbohydrates have, by far, been researched the most in their relationship to microbial diversity. Carbohydrates have a digestible and non-digestible component. The digestible are the monosaccharides and disaccharides that get broken down by enzymes of the body into simple glucose, fructose and galactose that the cells of the body can use. The non-digestible component is a complex oligosaccharide called fibre and resistant starches. We will return to these in the next chapter

Artificial Sweeteners

Chemicals such as aspartame, xylitol, saccharin, mannitol and others have been introduced to more and more foods with the aim to reduce global obesity and heart disease by replacing sugar. While some early studies showed that this actually worked, we now have few smaller studies on human specifically looking at glucose tolerance and microbiome. These studies are showing potential alteration and damage to the human gut microbiome which leads to worsened glucose tolerance and poorer insulin sensitivity (both are increased risk factors for diabetes, a condition that sweeteners are meant to prevent). While we don’t yet have sufficient data to say whether sweeteners damage microbiome or not, based on some early evidence caution would be advised. Personally, I advise my clients to stay away from sweeteners whenever possible (possible even Stevia), not to sweeten their drinks with anything and if needed to use natural ingredients such as honey for non-vegans or maple syrup (fructose-free) for vegans.


I’ve decided to include this in this chapter more for information purposes since there is nothing any of us can do with how we were born; however, if any of you reading this are to become mother or father, this information may be of use to you. Infants born through natural, vaginal birth acquire a sample of the maternal vaginal microbiome as they pass through the birth canal. Not only that, sometimes during the labour, women will actually defecate themselves (not cool, I know but this is actually one of mothers’ “first gifts” to the baby as gross as that sound) with this, the baby is now exposed to both vaginal and intestinal microbiota and these will be the first bacteria to colonise the baby’s gut, including the oral microbiota. Secondly, the first hours of breast-feeding, the mom produces a thickened and dense milk called colostrum which is literally a probiotic bomb further colonising the baby’s gut. A combination of natural birth & proper breast duration of breast-feeding (6 months +) set the baby for a perfect start to a healthy life.

When none of this happens and the baby is born c-section and/or fed by bottle and the first bacteria it comes in contact with are that of doctor’s and parents’ skin it gets a different starting microbiota and this may potentially develop things like allergies, asthmas even predispose the baby to autoimmunity. Same with baby formulas, it just isn’t the same thing. Not even close, we are far from having identified all the bacteria in the gut and breast milk, and so far we have not been able to replicate nature. Unfortunately, sometimes C-section has to happen for emergency reasons and sometimes breast-feeding isn’t an option and that’s ok; in those cases, for the safety of the mom and baby the c-section and bottle feeding need to happen without question, but as long as there is a choice, the natural form should be chosen.


I will probably make posts on these topics in the future as there is a lot of emerging research into the exposure to toxins from day to day life and from food. Suffice to say it is wise to avoid as many chemicals in life as possible. Many of them, such as BPA from plastic bottles, chemicals and phosphates from junk food, organochloride and organophosphate pesticides from sprayed crops, arsenic in water, cleaning products and others, may be damaging to the gut microbiome in ways we have not studied yet. Expect to hear more on these topics in the future.



In the Carbohydrate section above, we touched on the non-digestible, complex carbohydrates also known as fibre and resistant starches. These are also called prebiotics (with “e” not “o”) because they can feed our gut bacteria. Prebiotics are essentially food for our gut bacteria. The microbiome can break the fibre and resistant starches down and create short-chain fatty acids (SCFA, discussed in part 1) that have potent brain-enhancing, mood-improving, immunomodulating function. SCFA improve the health of the gut as well as the brain and enhance the overall gut-brain communication. They also have an important anti-inflammatory function and regulate the growth of pathogenic & opportunistic bacteria. Prebiotics are not the same as Probiotics. Where prebiotics ensure the existing gut bacteria are well provided for, the probiotics are actually real living bacteria. Regular consumption of prebiotics is also beneficial for people with asthma, allergies, inflammatory conditions, eczemas, psoriasis but also depression and other mental health conditions.

Some of the superior prebiotic foods are mushrooms (all types), beans, lentils, edamame beans, onion, garlic, kimchi, miso paste, natto, artichoke, unripe banana, green tea, black tea, broccoli, sweet potatoes, oats, apples, cauliflower, dandelion leaf, wheat germ, barley and buckwheat.


Looking at products such as kefir, kimchi, kombucha or your probiotic supplement, you would have come across words such as Lactobacillus or Bifidobacterium. These are the name of some of the known probiotic strains that can survive in food products. Probiotics are living species of beneficial gut bacteria condensed to a sterile environment (such as probiotic capsule) or to a living environment (such as kefir), and once they are consumed, the hope is that they will add up to existing bacteria in the gut and help the beneficial colonies to grow. However, the reality is different, and for the new bacteria to help colonise the gut, they need to come in dramatic amounts, in tens of billions per portion; otherwise, they simply won’t have the “power” to make space for themselves. You can imagine trying to storm a medieval castle armed with thousands of troops by sending an army of 20 farmers with pickaxes. What you need is 10 times the amount of defenders and superior gear and tactics. Probiotics in the food are useful but they generally add little to the existing microbiome diversity, and usually, large amounts are preferable of at least 50 billion CFU. Probiotics can be taken for a long time, even years.

How to use probiotics? : Probiotics, unlike other supplements can be used pretty much indefinitely. They are great support for overall digestion, immunity and brain. When using them pick a product that has a good complexity of a variety of bacteria, at least 10-20 different strains and don't go below 30 bilion Colony Forming Units (CFU). For general maintenance a good variety of Lactobacillus as well as Bifidobacterium is recommended. However if you have a severe gut health issue such as IBD, chronic pancreatitis, gastritis and similar it may be worth finding a specialist to help you create the gut protocol as certain strains can be applied therapeutically but need to be structured properly. Make sure to get good quality probiotics, not something cheap from the mall. Find a bran that does their own clinical research. Personally I am a great fan of Optibac (this is not a paid promotion) however they can be less accessible in certain countries so maybe speak to a doctor or a local expert to ask for suggestions.

Beneficial Foods

The diet that is beneficial for the rest of the body is usually also beneficial for the gut. All plant foods are good because they contain fibre and/or resistant starches. Adding vegetables, legumes, whole grains, seeds and fruits to the diet will provide greatly to your microbiome. Think more diversity than volume. Keep introducing new foods all the time, experiment with vegetables you’ve never tried before, try new fruits, remove some meat and add more legumes. At the same time, excessive amounts of meat, dairy and eggs can tip the balance of the microbiome so you want to make sure your food is predominantly based on plants with small amounts of animal food. Also, consider eating as few artificial sweeteners as possible.

Beneficial Drinks

Green tea & black tea both also have positive effects for certain phyla (largest colonies) of the microbiome. Other teas such as dandelion, chamomile, lavender, liquorice may also be helpful. Smoothies, as well as vegetable juices, may generally be useful. Coffee does have some benefits as well. Personally, I am not a fan of kombucha due to added sugar or artificial sweeteners and mostly very poor content of probiotics, so I cannot recommend it. However, enriched liquid dairy products are also good as long as they are low on sugar and free from artificial sweeteners. You can add turmeric to your coffee or tea for some extra anti-inflammatory benefit as well.


It would be advisable to eliminate all forms of destructive habits that harm the gut-brain connection. If you drink a lot, cut down on it. If you are a smoker, do your absolute maximum to stop. If you consume a lot of sugar and junk food, try to work on minimising that. If you take a lot of over the counter drugs, do your best to fix the underlying root cause rather than masking symptoms. If you are chronically stressed, take control of it by using meditation or deep abdominal breathing. If you lead a passive lifestyle, consider adding more exercise to your life.

Other ways to support your gut

Avoid eating too many times throughout the day. Every time you eat something your body has to start a whole digestive process which is very energy draining. Every time you digest, your gut-cleansing mechanism is switched off. Even a handful of salty peanuts is a sufficient trigger for this. Consume 3 main meals during the day but resist eating tiny portions of snacks in between or nibbling on sweets and salty snacks; this ensures that your gut’s self-cleansing mechanism called MMC (I may do an article on this in the future) is switched on between meals and the gut can clean & heal itself. Give yourself sufficient breaks between meals to build up your digestive juices and to optimise digestion.

Also, make sure to chew properly and consume your meals mindfully rather than on the go or in front of TV or laptop. Take your meals away from your desk and savour the taste properly. Finally, you may also add ginger, herbal spices, herbal teas and garlic to support your digestion. Sometimes doing these few simple things makes a profound difference to people’s digestive capacity.


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