Our Marvellous Microbiome

The digestive tract does more than just digest, absorb and eliminate; it houses our marvellous microbiome.

In recent decades scientists have made huge discoveries about our microbiome; you may know this as friendly bacteria or healthy bacteria or gut flora.

Current science acknowledges that the digestive system, particularly the microbiome, is intimately connected to every aspect of health, including our brain and mental health. (1) So headaches, anxiety, inability to concentrate, brain fog, and even a tendency to have a negative outlook on life can all be rooted in the state of the microbiome. Dr David Perlmutter, in his book Brain Maker, claims that the microbiome is as crucial to our well-being as oxygen and water. (2)

There are trillions of microorganisms living along our nine-metre digestive tract including bacteria, viruses, fungi and parasites. Mostly bacteria, more bacteria than cells in our entire body. These bacteria co-exist with us and participate in a wide variety of physiological actions so an imbalance in a person’s microbiome, known as dysbiosis, can impact our health in a variety of ways:

Low energy

The mitochondria in our cells can be damaged by inflammation brought on by a dysfunctional gut microbiome.

Low immunity

The gut microbiome trains our immune cells, showing the immune cells what is safe and which disease-causing microbes they should react to. A narrow range of microbiome is likely to overreact to safe microbes, leading to allergies and autoimmune disease or underreact to pathogens, opening the door to viruses. In addition, poor immunity allows inflammation throughout the body which leads to health problems. This includes damage from zombie cells.

Poor Nutrient Absorption

The gut microbiome controls our ability to absorb some nutrients, including the essential omega-3 fats, and produces some vitamins. The permeability of the intestines is protected by the gut microbiome; insufficient good bacteria can promote a “leaky gut”. Leaky gut refers to gaps in the tight junctions of the intestinal wall which are so small that we can think of them each as a microscopic space millions of times smaller than the head of a pin. When the intestinal barrier is compromised we are susceptible to various health conditions, through increased inflammation, often due to lipopolysaccharide (LPS) getting through the gaps in the single layer of epithelial cells into the bloodstream. (3)

Imbalanced hormones

The gut microbiome produces hormones that can affect our metabolism, immunity and behaviour. This interplay is bidirectional because the microbiome has been shown to be both affected by and to affect our hormones. When the gut microbiome is imbalanced our vital hormones become imbalanced.

Overworked liver

Less good bacteria to detoxify toxins in our food means more work for the liver.

Poor pain perception

People with an unhealthy microbiome may be more sensitive to pain.

Anxiety and depression

Stress-induced changes to the gut microbiome may affect the brain and behaviour. Research has found that defensive molecules produced by the gut during infection, called inflammatory cytokines, disrupt brain neurochemistry and make people more vulnerable to anxiety and depression. Neurotransmitters, including serotonin, are produced and released in the gut. This may help explain why more than half of people with chronic gastrointestinal disorders such as Crohn’s disease, ulcerative colitis and irritable bowel syndrome (IBS) are also plagued by anxiety and depression. (4)

Inflammatory joint pain and skin conditions

Beneficial bacteria in the gut microbiome help to control the body’s inflammatory pathways.

Gut and brain communication

Our gut and brain communicate. Think of the last time you felt worried or nervous, perhaps you had butterflies in your stomach or had to visit the toilet many times; this is your brain and gut communicating. Scientists used to think this communication was just one way – from brain to gut – but now we know the gut can also communicate with the brain. This happens through the vagus nerve, which goes from the brain stem to the abdomen, directing many involuntary bodily processes such as the heart rate and digestion. The microbiome directly affects the function of the cells along the vagus nerve. What we eat affects how we think.

The good news is that anyone can change the state of the microbiome through dietary choices; thankfully the microbiome responds to rehabilitation. The more diverse our diet, the more diverse and adaptable our gut microbiome will be and the greater benefit to our overall health.

How does this translate to what we eat? ‘Variety is the spice of life’ is a well-known saying and this is true for our diet – try to eat thirty different plant foods per week and keep trying new foods. If our plant food consumption is restricted then our microbiome will be restricted; because we are not feeding all the families some will starve and die out. We really are what we eat. Gradually introducing a diverse range of plant foods will build a diverse microbiome, a bit like building our immunity through small doses of germs, to build tolerance. If eating vegetables is difficult for you consider blending them into smoothies, steaming or roasting them for better flavour and retention of nutrients.

Thirty plant foods per week can be made up of wholegrains, fruits, vegetables, nuts and seeds, legumes (beans and pulses) and herbs and spices (including tea and coffee). Various herbs are found to positively influence the microbiome which indirectly influence insulin and glucose, to help regulate our blood sugar levels, through their effects on gut bacteria. (7) For example, traditional Chinese herbal products berberine and ginseng. Eat the rainbow every day to add maximum variety to your food and microbiome.

Eating vegetables and fruit from every colour of the rainbow adds diversity to the diet and microbiome

Gut bacteria differs from person to person depending on food eaten, medication (especially antibiotics, laxatives, and heartburn medication), health imbalances, and environment. Even identical twins have different gut microbiomes. (5) We know that our gut microbiome plays a role in activating and deactivating medicines, so this explains in part why people can respond in different ways to the same medication. We can think of our gut microbiome as our inner universe. And this is something we have control over – diet and lifestyle choices have a bigger effect on how healthy our gut microbiome is than our genetics do.

Nova Food Classification (6)

Nutritious whole food, including around 30g of fibre a day, promotes a healthy gut microbiome whereas processed and ultra-processed food and junk food allow harmful bacteria to take hold. Beneficial gut bacteria need fibre to feed on – a process known as fermentation – which produces short-chain fatty acids (SCFAs). These molecules maintain the integrity of the gut lining to stop unwanted pathogens from getting into the bloodstream. As well as influencing immunity these SCFAs play an important role in hormones, metabolism, heart and brain health.

In 2012 a study was published to show that people with type 2 diabetes suffered from bacterial imbalances (dysbiosis) in their gut. These imbalances caused them to lack important by-products from gut bacteria that are needed to maintain the health of the cells in the digestive system. Due to a disrupted gut microbiome, a cascade of events in the body can lead to diabetes and brain disease. (7)

Our lifestyle and environment also influence our microbiome including time spent in nature, gardening, animal and people exposure. So this explains the benefits of these activities on our health.

A Cheshire Nature Reserve

Use natural household cleaning and personal products, no harsh sanitising now! The skin also has a microbiome which we need to protect. Remember the traditional cleaning methods such as white vinegar for streak-free windows, lemon juice as a natural bleaching agent to remove stains, soda crystals to remove stains or clean inside the washing machine or drains, bicarb of soda to clean inside the fridge, pans, sinks, cookers and kitchen worktops.

How is your microbiome health? Is it healthy and dominated by beneficial bacteria? Or is it sick and overrun by bad, unfriendly bacteria?

Do you have any symptoms of bloating, gas, constipation, diarrhoea, abdominal pain, heartburn, acid reflux, fatigue, unintended weight loss or unexplained weight gain, sleep disturbances, skin irritations, autoimmune conditions, food intolerances, joint pain?

For help to create an optimum gut microbiome and positively influence your energy levels and health use the contact page and I will set up your free discovery call.


  1. Dr D Perlmutter Brain Maker 2015 p23
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9142943/ Anthocyanins in Chronic Diseases: The Power of Purple
  3. https://www.apa.org/monitor/2012/09/gut-feeling
  4. Dr Megan Rossi Eat More. Live Well 2021 p55
  5. Dr D Perlmutter Brain Maker 2015 p50
  6. https://www.frontiersin.org/articles/10.3389/fnut.2022.821657/full
  7. Dr D Perlmutter Brain Maker 2015 p51