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How your gut microbiome affects your health

The human gut microbiome is a complex ecosystem of trillions of microorganisms, including bacteria which live in our gut or gastrointestinal (GI) tract. Our GI tract includes our mouth, oesophagus, stomach, small intestine, large intestine and anus. The GI tract is a specialised barrier between the outside world and our body, digesting and allowing absorption of nutrients whilst recognising and stopping hazardous substances from entering our body and protecting against infections. Each region of the GI tract has its own specific function and distinct collections of microbes. Everyone's microbiome is different and is affected by things we can change like diet and medication, and things we cannot change, like our genetics and age.


The different types of microorganisms that live in our gut us affect our mental and immune health and influence the risk of developing chronic diseases like heart disease, cancer, Alzheimer’s disease, obesity and diabetes.


The establishment of an individual’s gut microbiome begins before birth - a mother’s diet affects her child’s gut microbiome and influences its risk of developing obesity and metabolic syndrome. The way a baby is born - vaginal vs. cesarean delivery - also makes a difference. Babies which are delivered vaginally have a healthier microbiome which in turn affects the development of its immune system and subsequent childhood allergies and autoimmune diseases. The importance of a healthy diet during the first years of life is also vital to establishing a healthy, diverse gut microbiome, a functional gut barrier and inflammatory protection. Babies which are breast fed also have a healthier gut microbiome versus those on formula, and delayed diversification of the microbiome during the first year of life is linked to allergy, asthma and malnutrition.


In a healthy person the gut microbiota includes both ‘beneficial’ bacteria as well as ‘bad’ bacteria, which cause no problems as they are in balance. With the wrong lifestyle choices however, we can disturb this balance and favour the growth of bacteria that are associated with poor health. Examples of poor lifestyle choices - include a low fibre diet, ultra processed foods, poor sleep patterns and inappropriate use of antibiotics. A reduction in gut microbiome diversity and loss of good bacteria is known as dysbiosis.


Dysbiosis can cause symptoms such as bloating, frequent bowel motions, spasms, and induce inflammation all around the body leading to aggravation of inflammatory conditions like arthritis and migraines.


The gut and the brain are in constant two- way communication; the nervous system in your gut is also known as our ‘second brain.’ Individuals with mental health conditions such as anxiety, depression, autism and schizophrenia, have a significantly different microbiome composition.


You can test the health of your gut microbiome by analysing your stool to enable the diagnosis of maldigestion, inflammation, dysbiosis, metabolic imbalances and infection. This can help your physician to prescribe interventions for the following conditions:

  • Maldigestion: apple cider vinegar, mindful eating (slow eating, chewing thoroughly), food choices (high fibre diet, green vegetables, avoid ultra processed foods).

  • Inflammation: identify food sensitivities, add anti-inflammatory spices such as turmeric, Omega 3 supplements.

  • Dysbiosis: pre and probiotics, high fibre diet.

  • Metabolic imbalance: increase fermented foods).

  • Infection: (antibiotic or anti parasitic prescription if required).

Indigestible fibre, found in vegetable and fruits cannot be broken down by our own enzymes, and is digested by the microbiota in the large intestine to produce short chain fatty acids (SCFAs). These play a vital role in maintaining normal barrier function of the intestine. If this intestinal barrier is compromised it leads to systemic inflammation.


Poor gut health can lead to a ‘leaky gut’. Our gut membranes usually keep out harmful substances, but when the gut is leaky, for example because of a poor diet, harmful products from bacteria called lipopolysaccharides enter our blood causing inflammation all over our body - metaflammation. This chronic inflammation increases the risk of the chronic diseases of ageing as well as affecting mental health.



As microbiota are so vital to our health it is important to ensure that we maintain and promote a healthy, diverse range of bacteria. Getting enough fibre from varied whole, plant-based foods especially vegetables, is key. We can support increased levels of SCFAs by eating foods which are naturally high in prebiotic fibres. These include raw onions, leeks, bananas, seaweed and asparagus but also all fruits, vegetables, beans and wholegrain oats and barley. Also, probiotic foods help populate and diversify our gut microbiome as they contain live bacteria. Probiotic foods include kefir, yoghurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi and miso.


Find out more about the Longevity Annual health check and download the longevity doctor guide to healthy living.



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