For many, the thought of bacteria reminds them of disease or getting sick, but it is important to know that there are billions of beneficial bacteria within all of us. Bacteria make up our microbiome which is our integral internal ecosystem that benefits our digestive health, immune system and beyond.

The scientific community is currently embracing the essential role that bacteria have in keeping us healthy as well as fostering a strong immune and mental health system.

What is the Microbiome?

The Microbiome is a complex internal ecosystem of bacteria or a community of microbes within our bodies and digestive systems. The bacteria that make up our microbiome is located throughout the whole body and have various roles which help to govern many bodily systems and functions. Some researchers even believe that up to 90% of disease can be traced back to the microbiome and gut health. This is because poor gut health has been linked to dementia, arthritis, autoimmune diseases and more.

Research done by The University of Utah Genetic Science Learning Center has shown that “the human microbiome (all of our microbes’ genes) can be considered a counterpart to the human genome (all of our genes). The genes in our microbiome, therefore, outnumber the genes in our genome by about 100 to 1.” (Genetic Science Learning Center, 2014). This means that when we understand the microbiome better, symptoms of all sorts of ‘genetic diseases’ could be treated, cured or prevented.

Why Gut Health is Essential to Mental Health

Many scientists believe that the microbiome has a huge impact on how we feel as well as our state of mind. The gut-brain relationship seems to be bidirectional as the microbiome is responsible for producing neurotransmitters and other neuroactive compounds that act on the brain. The brain also acts on immune and gastrointestinal functions that help to shape the microbial makeup of the gut. These interactions mainly occur via the vagus nerve, which connects the digestive tract and brain. It’s quite interesting, though, that about 90% of the fibres in the vagus nerve, carry information from the digestive tract/microbiome to the brain/central nervous system, and not the other way around (Schmidt, C, 2015).

Friendly gut bacteria are also seen as natural anti-anxiety and antidepressant organisms as they help to manage neurotransmitter activity (Gonzalez, A et al, 2011). Our diets greatly affect our microbiome which in turn affects neurotransmitter activity and therefore our energy levels, our ability to handle stress and how we feel (Schmidt, C. 2015).

According to Patrick Holford (2010), a healthy digestive system is responsible for producing most of the body’s serotonin, also, the presence of probiotics (good bacteria) promote cytokines (immune-transmitters) and assist them in reducing inflammation and signalling to the brain to reduce stress reactions. Probiotics also boost ‘brain-derived neurotrophic factor’ which is something that makes the receptors in the brain more responsive to neurotransmitters. A study published in the European Journal of Clinical Nutrition (D. Benton, et al.2007) shows the effect of probiotics on improving the mood of depressed patients. Another study (Pinto-Sanchez et al, 2017) showed a correlation between depression and gut health when 60% of patients who took part in the study reported decreased depression after taking probiotics daily for 6 weeks.

When the brain is in destress it directly communicates with the gut which then promotes inflammation and shuts down digestion. This has been studied when baby rats were separated from their mothers, but the stress response was reduced and the system was reset when given probiotics (M. G. Gareau, et al. 2007).

Microbiome & Immune System

A properly functioning digestive system and healthy microbiome are also essential when it comes to a healthy immune system. This is because up to 80% of all immune cells are located in the gut (Holford, 2010). Gut microbes are needed to make vitamins, break dietary fibre into digestible short-chain fatty acids and govern normal functions in the immune system (Schmidt, 2015).

Methods to Establish a Strong Microbiome

The good news is that there is plenty we can do to keep our microbiome healthy and flourishing:

  • Avoid Antibiotics as Much as Possible: they eliminate good bacteria, which means they lower immune function and raise the risk for diseases, infections and allergies. Antibiotics surely have its place and have saved many lives, but unfortunately, they are often overprescribed and misunderstood.
  • Eat fermented/probiotic-rich foods, such as apple cider vinegar, yoghurt, kimchi, sauerkraut and kefir. Eat at least one serving per day.
  • Vitamin B6 impacts the production of serotonin and neurotransmitters and are associated with positive mood and reducing stress (McCarty, 2000). It has further also been used to treat depression and other mood disorders (Hartvig et al, 1995). The shiitake mushroom contains a high dose of vitamin B6 and other food sources include avocados, chicken, brown rice, eggs, sunflower seeds, oatmeal and walnuts.
  • Chew your food. By chewing your food properly more enzymes are secreted to aid in the digestive process.
  • Give the digestive system a rest. The migrating motor complex sweeps the gut only after 3-4 hours of fasting and then occurs every 2 hours until you have a meal again. It is important to leave enough time between meals for this essential process to take place.
  • Avoid alcohol. Alcohol destroys good bacteria and could contribute to different digestive disturbances such as yeast and bacterial overgrowth, leaky gut and SIBO (Munoz, K, 2017).
  • Variety is key. Different types of microbes like different types of food. Eating a wide variety of food, especially plants is one of the best things you can do to keep your microbes happy. Aim for up to 40 different whole plant foods, spices and herbs each week.
  • Soak beans. Beans are hard to digest as they contain phytic acid which limits the ability to absorb the available nutrients. Beans can be soaked for up to 12 hours to reduce phytic acid. Red lentils are easy to digest and can be used more often.
  • Avoid sugary snacks. A study done by Holford (2010) shows that a high sugar-based snack consumption (three or more sugary snacks a day) doubles the likelihood of poor mind and mood health.
  • Avoid caffeine as it worsens mental performance. A study published in the American Journal of Psychiatry found that high and moderate consumers of coffee had higher levels of depression and anxiety than abstainers. The high consumers also had lower academic performance and more stress-related medical issues (Holford, 2006).
  • Avoid vegetable oils, processed grains and refines carbohydrates, dairy and trans fats as they are all pro-inflammatory foods.
  • Include: Fresh fruit (not juice) such as strawberries, pomegranates, oranges, cherries, blueberries & blackberries (as it contains a lot of antioxidants); fresh vegetables (contains a lot of phytonutrients) including kale, spinach, cabbage, broccoli, cruciferous vegetables, carrots and beets; herbs & spices such as thyme, oregano, basil, ginger and turmeric; omega 3 fatty acids and other healthy fats including wild-caught fish, grass-fed meat, cage-free eggs, walnuts, chia seeds, pumpkin seeds and coconut oil.
  • Avoid gluten. Gluten negatively affects the blood-brain barrier, makes the gut lining more leaky/ permeable and allows unwanted food particles, toxins and more to enter the bloodstream. As they don’t belong in the bloodstream the immune system gets sensitised which promotes autoimmunity and inflammation (both play a role in the progression and development of brain-related diseases).


Barreau, F. et al. 2004. ‘Neonatal maternal deprivation triggers long term alterations in colonic epithelial barrier and mucosal immunity in rats’, Gut, April 2004;53(4):501–6)

Benton, D, et al.2007. ‘Impact of consuming a milkdrink containing a probiotic on mood and cognition’, European Journal of Clinical Nutrition, 2007;61(3):355–61

Gareau, M.G et al. Probiotic treatment of rat pups normalises corticosterone release and ameliorates colonic dysfunction induced by maternal separation’, Gut, 2007;56:1522–8

Genetic Science Learning Center. “The Human Microbiome.” Learn.Genetics. August 15, 2014. Accessed August 26, 2020.

Gonzalez, A, et al, 2011, The mind-body-microbial continuum, Dialogues in Clinical Neuroscience, 2011 Mar; 13(1): 55–62.

Hartvig P, et al, 1995. Pyridoxine effect on synthesis rate of serotonin in the monkey brain measured with positron emission tomography. J Neural Transm Gen Sect. 1995;102(2):91-97. doi:10.1007/BF01276505

Holford, P. 2006. Optimum Nutrition for your Child’s Mind, pg 33.

Holford, Patrick. 2010. The Feel Good Factor: 10 proven ways to boost your mood and motivate yourself (p. 230). Little, Brown Book Group. Kindle Edition.

McCarty MF, 2000. High-dose pyridoxine as an ‘anti-stress’ strategy. Med Hypotheses. 2000;54(5):803-807. doi:10.1054/mehy.1999.0955

Munoz, K. 2017. The Gut-Brain Connection: What Remedies Can Both Heal & Improve It?

Pinto-Sanchez MI, Hall GB, Ghajar K, et al. 2017 Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients With Irritable Bowel Syndrome. Gastroenterology. 2017;153(2):448-459.e8. doi:10.1053/j.gastro.2017.05.003

Schmidt, C, 2015. “Mental Health: Thinking from the Gut” in Scientific American 312, 3, 97-100 (March 2015).

Related Blog Posts

    Your Cart
    Your cart is emptyReturn to Shop