Did you know that a healthy gut is crucial to your happiness? 90% of your serotonin, the neurotransmitter that enables you to feel happy, optimistic and self-confident, is produced in the gut and the health of your gut directly influences your serotonin levels.

But it’s not just about serotonin. The gut bacteria both produce and respond to other chemicals that your brain uses to create thoughts and feelings, such as melatonin, dopamine, noradrenaline, GABA and acetylcholine.

This is all confirmed by the findings of the Human Microbiome Project which clearly shows that the gut has a profound impact on the brain. This article will give you an idea of what may be happening in your body when you’re not feeling happy as well as some nutritional tips to start addressing that.

One caveat before we dive in: to achieve the best health results, your nutritional therapy needs to be personalised based on your unique medical history, genetic makeup, lifestyle and environmental exposures. The following is simply a generalised overview of the therapeutic strategy for gut health. But before I tackle that, here’s the rationale that links your happiness, or lack of it, to your microbiome.

An ever-growing number of studies have demonstrated that one big contributor to low mood, depressive states, anxiety, lack of stamina and poor resilience to stress is a disturbance in the natural human flora in the gut (dysbiosis).

Considering this strong connection between the brain and the gut, we can safely argue that the brain and the microbiome function as one system. Here’s some of the jobs that your gut bacteria perform for you:

  • synthesise neurotransmitters (serotonin, dopamine), the very chemicals which your brain uses to regulate thought and emotion
  • produce B vitamins (B12, folate, niacin), vital for brain health, as well as vitamin K
  • produce of the short chain fatty acid butyrate– a fuel for the brain, and acetate involved with appetite regulation
  • communication with the brain via the vagus nerve
  • genetic expression: bacteria can turn genes on and off (epigenetics)
  • digestion of food
  • protection against pathogens through crowding and competition
  • regulatory effect on your the immune system, 75% of which is found in the gut
  • maintenance of your ideal weight by regulating your appetite and metabolism

Research also shows that a person’s emotional state and stress levels can negatively alter the function of the gastrointestinal tract due to altered brain signalling to the gut.

Having an unhealthy microbiome means both a lack of diversity in bacterial strains as well as an overgrowth of pathogenic or opportunistic microorganisms. Unfortunately this is an extremely common clinical occurrence and an almost unavoidable consequence of our modern lifestyle.

Your microbiome is crucial in determining whether your gut can produce the right brain chemicals in the right amounts. A microbiome that is out of balance can cause you to feel anxious and depressed. It can keep you from thinking clearly, it can disrupt your concentration and interfere with your memory.  Conversely,  having a healthy microbiome is key to feeling calm, focused, energised and optimistic.

Thus, it’s in your best interest to look after your microbiome and keep dysbiosis at bay. Here’s what may cause it:

  • poor diet
  • NSAIDs (pain and fever medications): ibuprofen, aspirin
  • antibiotics
  • mold exposure
  • Lyme infection
  • thyroid disturbance & other hormonal imbalances
  • environmental pollutants: PCBs, lead, mercury (amalgam fillings), perchlorates
  • chronic stress
  • nutrient deficiencies
  • Cesarian birth

Another mechanism for how an unhealthy microbiome can make you miserable is inflammation triggered by leaky gut, in which undigested food escapes from the damaged intestinal wall and triggers system-wide inflammation. Inflammation can easily disrupt the brain chemistry, with dire consequences such as depression, cognitive decline and other neurological symptoms. Leaky gut leads to high levels of histamine, ammonia and inflammatory chemicals in the body that damage the sensitive blood brain barrier, thus allowing toxic compounds into the brain (experts are now talking about “Leaky Brain”).

But dysbiosis can produce a wide range of symptoms and can contribute to many illnesses, many of which seem unrelated to the digestive system. Having two or more of the following symptoms should be a red flag that you may have dysbiosis:

Digestive  Brain-related Metabolic Skin Various
Bloating/gas Anxiety Autoimmune disorders Acne Decreased immune function
Constipation Depression Cancer (lymphoma) Skin blemishes Joint & muscle pain, CFS
Diarrhea Mood swings Cardiovascular disorders Eczema


Irritable bowel syndrome, Celiac Disease Autism  Diabetes Psoriasis  Obesity
 Heartburn Low resilience to stress Hypothyroidism  Rosacea  Bad breath

Diet plays a critical role in the health of the microbiome. A number of foods—including those containing sugar, unfermented soy, gluten, and conventional dairy—can contribute to leaky gut and constant inflammation which disrupts the delicate balance of microorganisms in the gut resulting in dysbiosis and creating even more inflammation in a very damaging vicious cycle.

Conversely, not eating enough of the foods required to nourish the microbiome can also lead to all kinds of health problems.


If you have any doubts about that, check out this breakthrough Harvard study that showed that diet has not only a huge but an almost immediate effect on gut bacteria. The researchers fed volunteers two very different diets. One group was given a high-protein diet consisting of bacon and eggs, spareribs, brisket, salami, cheese, and pork rinds. The other was fed a very high-fiber diet of vegetables, grains, beans and fruit. Bacterial analysis of fecal samples collected before, during, and after the experiment.

In just 24 hours, a rapid microbial shift was observed: each group began to develop the very type of bacteria that would most help them digest the particular types of food they had just eaten. This obviously shows that different foods create a different microbiome and that, as long as our diet supports our microbiome, we can enjoy quite a bit of flexibility in our diets.

Foods to avoid for a healthy microbiome

To develop a healthy microbiome, you don’t want to eat too much meat  because studies have shown that much meat is detrimental to the microbiome. Thus the 55 percent of daily calories that some Paleo experts recommend might not be a good idea long-term. At the same time, you don’t want to consume a typical Western diet (refined flour, sugar, unhealthy fats, additives, preservativesartificial sweeteners) because these ingredients also feed the wrong kinds of bacteria.

Foods you should eat for a healthy microbiome

The best diet for a healthy microbiome is one that contains a lots of fresh, whole vegetables and fruit, legumes, and small amounts of whole grains (only if you’re not gluten-sensitive or have an auto-immune condition). These are terrific “microbiome food”, also called “prebiotics”: foods that have exactly the kind of fiber that feed many beneficial species: asparagus, carrots, garlic, Jerusalem artichokes, jicama, leeks, onions, radishes, tomatoes.

Why you absolutely need PREBIOTICS

Bacteria require food and nutrients to feed on so they may colonise and proliferate. Prebiotic fibers are the foundation of a healthy microbiome. These are components of food indigestible to us yet fermentable by bacteria. In the process, the bacteria produce metabolites called short chain fatty acids which have a number of protective and nourishing roles in the human body.

Some of the benefits of prebiotics include improvements in stress and anxiety . Currently there are many prebiotic products on the market including a wide range of fibers like larch arabinogalactan, inulin, pectin, oligofructose, fructooligosaccharides (FOS), galactooligosaccharides (GOS), and other oligosaccharides. Acacia fiber offers a wealth of health benefits from lowering cholesterol, aiding in sugar regulation and normalising bowel function.

Fermented foods are a must : kimchi, raw sauerkraut, fermented vegetables, and kefir (a type of fermented milk) are natural probiotics that replenish your friendly bacteria. To be consumed daily.

Dietary polyphenols – also a must

Recent studies indicate that dietary polyphenols contribute to maintenance of gut health by increasing species diversity and stimulating growth of beneficial bacteria (i.e., faecalibacterium, lactobacilli, and bifidobacteria) while inhibiting pathogenic bacteria such as C. perfringens and C. histolyticum.

The long-term health benefits associated with the Mediterranean diet over other types low-fat diets may well result from higher levels and variety of natural polyphenols in Mediterranean foods: olives, capers, oregano, rosemary, sage, thyme, cumin, caraway,  hazelnuts, blueberries, pecans, walnuts, plums, cherries, artichoke, chicory, ginger, almonds, red onions, spinach, shallots, extra-virgin olive oil, peaches, oranges, pears, endive, beans, broccoli, lemon juice, grapes, carrots, vinegar, rosé wine, white wine. Check out this table in the European Journal of Clinical Nutrition showing the 100 richest foods in polyphenol and antioxidant content.

What if your microbiome is imbalanced?

The above nutritional advice applies if you’re in perfect health and only interested in maintenance. If your microbiome is already partially compromised, you might have to go on an elimination diet for 2 to 4 weeks in order to attenuate the immune response triggered by reactive foods.

Without testing, it’s almost impossible to say what foods you’re reacting to as it can be anything that contains proteins. However, blood tests show that the usual suspects are:

  • gluten (in wheat, barley, rye and other grains;used as a preservative in salad dressings, soy sauce, ketchup etc)
  • soy (also used as a preservative in processed foods : baked products, hamburgers, cereals, chocolate)
  • eggs
  • dairy
  • corn

Some immune reactions happen immediately and severely. Others, such as those involved in food sensitivities, take hours or days to develop (delayed response) therefore it is difficult to link specific foods to symptoms. Signs that your immune system is reacting to foods can range from acne, sore throat, brain fog  to bloating, gas, aching joints, increased appetite, food cravings, weight gain, lack of energy, problems with sleep.

At the end of 4 weeks, you should reinoculate the GI tract with fermented foods. Fermented foods such as sauerkraut, kimchi, fermented vegetables, yoghurt, kefir are natural probiotics. But start slowly if you’re not used to them (e.g. one tablespoon of sauerkraut per day) in addition to taking probiotics in pill form.

NB: The sauerkraut shouldn’t be pasteurised as the pasteurisation process destroys its probiotic value. Unfortunately most shop-bought products are pasteurised.  Click here to learn how to make sauerkraut at home.


The easiest and fastest way to replenish your microbiome is to take probiotics in pill form. Research has shown that specific strains of bacteria have specific therapeutic actions. This means they can be used in a targeted approach and I’ll touch on that a little bit below.

Depression and Anxiety

Bifidiobacterium and Lactobacillus have been shown to improve a number of neuropsychiatric disorders and dysfunction including anxiety, depression, OCD and memory decline. A recent clinical study found that probiotics including both Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 are some of the most effective anxiolytic strains found to significantly reduce anxiety, depression and cortisol levels when taken together in just 30 days.

L. rhamnosus JB-1 was also found to reduce stress, anxiety and depression related behaviour in mice undergoing a series of stress tests. Research here highlighted the crucial role of bacteria in the bidirectional communication between the gut and brain and their importance in treating stress-related disorders including depression and anxiety.

Additional strains like L. casei and L. acidophilus were found to work on depression specifically as well as B. infantis,  B. bifidum, B. breve and L. plantarum PS 128 . The latter not only decreases anxiety and depression, it also improves various neurotransmitters related to these disorders and has psychotropic effects improving stress, neuropsychiatric disorders and neurodegeneration. For best results, use products that contain one or more of these strains.

Brain Fog  & Cognitive Decline 

High ammonia is a major contributing factor involved in symptoms like brain fog, difficulty comprehending and thinking. Studies in this realm often focus on liver conditions which impair its ability to detoxify creating high levels of this toxic compound. An unhealthy microbiome also creates high levels of ammonia. B. infantis, B. breve, L. acidophilus, L. rhamnosus, L. plantarum, L. casei, S. thermophiles and S. boulardii are all shown to improve signs and symptoms of cognitive decline and help to reduce ammonia levels.

General lack of wellbeing & chronic inflammation

If you have a general sense of lack of wellbeing, it’s highly likely that inflammation is part of the picture. Blood testing is recommended to track changes in inflammatory markers including CRP, ESR, IL1, IL6, IL8 and TNF-alpha.

Chronic inflammation and dysbiosis go hand in hand, laying the foundation for all of today’s chronic health conditions including brain disorders, heart conditions, thyroid problems, blood sugar imbalance and even cancer.  One of the best strains proven to bring down high levels of inflammation is Bifidobacterium infantis 35624. Three random, double blind trials concluded it works to bring down inflammation in both GI and non-GI issues, modulates the inflammatory response and decreases inflammatory cytokines.

Another common cause of inflammation is high levels of lipopolysaccharides (LPS) which are molecules found within the cell wall of Gram-negative bacteria. While these organisms normally reside in the intestine at a low level, unfavourable conditions like high stress, poor diet and poor health may trigger overgrowth and gut permeability, allowing LPS to leak out into the body setting off inflammatory and immune responses. In studies, L.reuteri, L. rhamnosus, L. plantarum, Bifidobacterium animalis, B. bifidum, B. longum, and B. longum subsp. Infantis were all found to greatly reduce levels of LPS while B infantis was found to be highly beneficial in lowering the inflammatory marker TNF-alpha.

GI Disorders: intestinal permeability (leaky gut), Crohn’s, ulcerative colitis

Bifidobacteria play a key role in the health of the large intestine and colon. Specifically B. lactis, BI-04, B. bifidum BB-06, B. lactis Bi-07, B. lactis HNO19 and B. breve BB-03 help to reduce bloating, decrease transit time and constipation, lower inflammation and regulate the immune system.

Lactobacillus casei gg. was found to protect against a variety of gastrointestinal diseases. In cases of Crohn’s disease,   it improves immune function considerably.

For leaky gut, B. longum, L. plantarum, L. reuteri and L. rhamnosus GG were demonstrated to increase tight junctions between intestinal cells, fortify the intestine wall and support healthy immune function.

Inflammatory Bowel disorders are very common. Studies looking at ulcerative colitis found great improvements in bowel function and decreases in long-term inflammation using a mixture of Bifidobacterium Longum BB536 plus the prebiotics Inulin and FOS

For  constipation, the beneficial strains include Bifidobacterium lactis DN- 173 010 found in yoghurt; S. boulardii, L. acidophilus LA5, L.paracasei ( l. casei 431) and Bifido BB12. 

Candida albicans

Yeast can be challenging to eliminate for some. A multiple-strain probiotic plus the enzymes Beta Glucanase and Hemicellulase were found beneficial in displacing and purging unwanted bacterial and yeast cells from the intestine, soothing and regulating inflammation.

Auto-immune Diseases

Saccharomyces boulardii is one of the most powerful and useful organisms to help reduce inflammation, remove unwanted yeast and regulate the immune system, even quieting the dysfunction found in autoimmunity. For patients suffering with any type of autoimmune condition, this strain must be part of the daily routine.

Weight Gain

The latest research is showing  that caloric restriction doesn’t work for weight loss so your should stop starving yourself. Even if people lose weight following the latest diet craze, the weight comes back on as soon as they start eating a normally again. That’s because the crucial factor is NOT the total number of calories you consume, but how your body responds to those calories.

A healthy microbiome is crucial for weight maintenance: it harvests your calories, extracts vitamins, decides whether you feel hungry or full and regulates your metabolism towards either fat burning or fat storage. On the other hand, an unhealthy microbiome will overpower you with cravings for sugar and unhealthy fats.

Studies show that weight gain correlates with low microbial diversity and some scientists, such as Martin J. Blaser, the director of the Human Microbiome Program at NYU, even argue that the destruction of the microbiome is the prime cause behind the obesity epidemic. Considering that we lose microbial diversity with every generation, fixing the microbiome should become a priority in clinical care.

Lactobacillus plant strain Number 14 has been shown to reduce the size of fat cells and induce weight loss.

Decreased resilience to stress

The microbiome is so sensitive to stress that even a 24 hour span of increased stress was shown to change the bacterial populations in the gut: the health-promoting bacteria die and the more resilient pathogenic strains move in to take their place.

Stress is not only the cause of an unhealthy microbiome but also its consequence: when you have dysbiosis, you just don’t feel right and an imbalanced microbiome decreases your resilience to stress further. This is how stress leads to more stress.

Stress also plays havoc in your hormonal system with the result being an excessive accumulation of belly fat. This is something that not too many people are aware of: while dietary sugar drives visceral fat (fat around your organs such as the liver), it is stress that drives abdominal fat. This is one way in which stress impacts not only your mood (via the microbiome) but also your figure. Double disaster!

On the bright side, Bifidobacterium species have been shown to positively influence the stress response and its associated psychiatric disorders in an anxious mice model.

In 2013, Tillisch et al, found evidence that consumption of a fermented milk product affected brain activity in healthy women. They processed emotions better, sensory regions were less active and they were better able to deal with stressors.

All these studies strengthen the role of gut microbiota supplementation as psychobiotic-based strategies for stress-related disorders, opening new avenues in the field of neurogastroenterology.

I generally recommend a multiple strain soil-based probiotic since studies find benefit in using multiple strains together.

I hope this article succeeded in shedding more light on the incredible complexity at play in the gut-brain axis. It’s quite fascinating when you think of it: because microorganisms were present as we evolved, our genes did not need to encode all of our vital information. That’s why the genes of our microbiome outnumber ours by a factor of 150 to 1 and they are there to perform an essential function that brings to mind the concept of symbiosis, of living together. We evolved as interdependent on microbial life. Microorganisms perform many tasks for us, from digestion to immunity, processing thought and emotion. To wipe them out without replenishing them can have dire consequences on your health. That’s why looking after your microbiome is one of the best prevention tools you should start applying today.

For more information, read this fascinating book on the microbiome by Raphael Kellman, MD. And you’re welcome to contact me at: