One of the best ways to take control of your health and wellbeing is to learn more about what’s really going on inside. By arming yourself with all the facts, you empower yourself to make healthy choices. So, we asked YourGP’s Dr Phimister to cut through the medical terminology and jargon to provide an overview of something that is crucial to everyone’s health – the microbiome. Read on as he delves into the science and answers some of your most common questions.

What is the microbiome?
The microbiome consists of all the microorganisms in the body. They are mostly bacteria that live in a symbiotic relationship with our body. They are located mostly in the large intestine, but are also found on the skin, mouth, ears, nose, respiratory tract, urinary tract, small intestine, vagina and even the stomach. The estimated number ranges from 10-100 trillion, which is more than the 30 trillion cells in the human body!

How does your microbiome first develop?
A baby is first introduced to the microbiome on its entrance to the outside world. Passage through the birth canal is advantageous to bring these normal healthy bacteria to cover the entire skin and other locations like the ears and nose.

Breastfeeding gives the perfect food for the baby with nature’s own water, protein, lipid, and carbohydrate mixture, along with minerals and vitamins, plus contact with skin flora bacteria on the breast. Over time, the food of the newborn and bacteria from the breast will shape the microbiome, influencing the immune system, digestive system and brain development.

Why is the microbiome so important?
The microbiome is essential for our health as we depend on its existence for our survival! They depend on us and us on them in a symbiotic relationship. The immune system is in constant surveillance for pathogens and toxins in the intestinal tract, more than any other place in the body. A healthy microbiome reduces stress on the immune system allowing it to function normally, which is essential for preventing autoimmune conditions, allergies and chronic inflammatory conditions like asthma, inflammatory bowel disease, heart disease and neurodegenerative conditions.

What is the best way to look after your microbiome?
The best way to look after your microbiome is to eat healthy nutrient-dense foods and healthy sugar-free drinks or water. Exercise daily or every other day and remember that relaxation and sleeping 7-8 hours a night are key elements of microbiome care, as well as living in harmony with your environment. Daily meditation is recommended too.

Are there any foods you should limit / avoid to protect your microbiome?
Food to avoid or limit to help your microbiome include processed and packed foods as well as wheat and gluten products like baked goods, bread, pasta and pizza. Grain-fed meats and poultry, and farmed fish should also be avoided or limited, as should partially hydrogenated fats like margarine and oils for cooking. Cow’s milk, ice cream and northern European cheeses should also be reduced or eliminated from the your diet, as well as snacks like sweets, milk chocolate, crisps, and sugary drinks including fizzy, diluting and fresh fruit juices.

What is the difference between prebiotics and probiotics?
Prebiotics feed the microbiome, like fertiliser feeds the soil. Prebiotics are mostly undigested fibres. These are found in vegetables such as onion, garlic, leeks, spring onion, asparagus, Jerusalem artichokes, savoy cabbage, and green peas; legumes such as lentils, chickpeas, red kidney beans and baked beans; fruits such as apples, nectarines, grapefruit, watermelon, pomegranate; grains such as rye bread, bran, wheat bread, pasta, oats, couscous; nuts and seeds such as almonds, pistachios, and flax seeds; and human breastmilk.

Probiotics promote the health of your microbiome and make up the microbiome too. The most common ones studied are lactobacillus and bifidobacterium, which are common in probiotic supplements bought from health food stores, pharmacies or online. The number of probiotics range from 10 to 50 billion species in one capsule and no scientific recommendation exists for the optimal dose.

Would you recommend taking daily prebiotic and probiotics supplements?
I recommend a high fibre diet to get all the prebiotics needed for your health. I don’t recommend prebiotic supplements in the long-term, preferring to optimise the diet with food that optimises the microbiome.

I recommend probiotics supplements for 1 month if you take an antibiotic for an infection. Otherwise, I recommend a variety of fermented foods, ideally to be eaten with each meal daily, such as high fat yoghurt (to avoid the low fat AKA high sugar yoghurt), kefir, goats cheese, sauerkraut, kimchi, miso, kombucha, tempeh or red wine.

What effect can antibiotics have on the microbiome?
Antibiotics will deplete some of the healthy microbiome and may give symptoms of diarrhoea, bloating, or indigestion. In severe rare cases, inflammation, bloody diarrhoea and clostridium difficile infection can result from antibiotics, especially long-term courses or recurrent use, typically in the elderly, resulting in hospital admission, sepsis, further antibiotic treatment and even death.

Discover more
If you would like to speak to Dr Phimister about improving your microbiome and / or your overall health, just email reception@your.gp or call us on 0131 225 5656 and we’ll be happy to arrange an appointment at a time that suits you.

References and resource links
• Defining the Human Microbiome, Luke K Ursell, Jessica L Metcalf, Laura Wegener Parfrey, and Rob Knight, 2013

• The Infant Microbiome: Implications for Infant Health and Neurocognitive Development, Irene Yang, PhD, RN, Postdoctoral Fellow, Elizabeth J. Corwin, PhD, RN, FAAN, Associate Dean and Professor, Patricia A. Brennan, PhD, Professor, Sheila Jordan, RN, MPH, Graduate Student, Jordan R. Murphy, BS, Nursing Student, and Anne Dunlop, MD, MPH, Associate Professor , 2016

• The Microbiome, Harvard T. H. Chan School of Public Health

• Clostridium Difficile Infection, NHS