Looking after your gut health by looking after the microbiome

More and more research is showing how important the health of the gut is to physical and mental well-being. The bacteria, yeast and viruses that live in our gut are called the gut microbiome and there are around 100 trillion of them.  Many of these microbes are beneficial, and even essential, to human health while others can be harmful. 


The gut microbiome is delicately balanced and the number of good bacteria can easily diminish and/or can be taken over by more harmful bacteria.  By reducing factors that harm the good microbiome and increasing factors that help it to be restored to the right balance, we can do much for our well-being. 

What does the right microbiome help with?

  • Reduces risk of metabolic disorders such as high cholesterol levels and diabetes; it can help normalise blood glucose levels.
  • Reduces risk of getting certain cancers including colorectal cancer.
  • Helps boost the immune system and reduces inflammation. The gut is the largest immune organ of the body, with over half of all immunologically active cells in the body located around the gut.  

As we age, the immune system works less efficiently, but encouraging a healthy microbiome can increase immunity.

  • The good bacteria can bind to sites on the layer of cells lining the gut and provide a barrier preventing penetration by toxins, adhesion and infiltration by harmful bacteria. This ‘contra-biotic’ effect can inhibit the sensitisation of the gut and may help prevent the symptoms of IBS
  • Break down toxic substances taken in with food.
  • Reducing the incidence and severity of a wide range of human diseases, including obesity, psoriasis, autism and mood disorders.
  • Increases the effectiveness of vaccinations This is important as people get older, as the immune system works less well (called immunosenescence).
  • Reduces anxiety and depression as there is a link between the brain and the gut (known as the gut-brain axis).
  • Attenuates levels of blood glucose and blood fats after a meal and through this action may help to reduce inflammation
  • Helps change certain plant oestrogens (from foods such as soya) into a more effective plant oestrogen called equol. During menopause, equol can exert a weak oestrogenic effect thus possibly lessen some menopausal symptoms such as hot flushes and also protect bone health. 
  • Helps with absorption of essential minerals. Many minerals are easily inhibited from being absorbed, such as iron and calcium, but when the right microbiota is present, their absorption is enhanced.
  • Inhibits pathogenic bugs from colonizing the gut, or at least weakens them, thus reducing stomach upsets and diarrhoea. Such bugs include norovirus, C difficile, Campylobacter, Escherichia coli (E. coli), Salmonella and Shigella.
  • Helps synthesize certain vitamins namely vitamin K (half of our requirement is provided by gut bacteria) plus B vitamins and vitamin C. 
  • Protects infants from allergies and related conditions such as asthma and eczema. 

What can lead to an unhealthy microbiome? 

  • A diet high in animal and processed foods, alcohol and sugars is associated with higher levels of intestinal inflammatory markers. This is due to increasing numbers of bacteria associated with poorer health such as Firmicutes, Ruminococcus species of the Blautia genus, and decreasing numbers of bacteria associated with good health such as commensals that produce short-chain fatty acids. The presence of short-chain fatty acids (SCFA) such as butyric acid is a sign of a healthy gut; this is because SCFAs improve the gut health through a number of local effects, including maintenance of the intestinal barrier integrity, mucus production, protection against inflammation and reduction of the risk of colorectal cancer.
  • A diet high in saturated fats and salt.
  • An unbalanced diet; so if you shun carbs and eat more fat and protein instead, you will be depriving the gut microbiota of the food they need to stay in sufficient numbers and diversity in your gut
  • A diet high in meat: research suggests that people who consume a lot of animal protein may suffer harmful changes in their gut microbiome and have higher risks of inflammatory bowel disease (IBD), a chronic inflammatory condition. Red meat may be especially unhelpful, as it raises levels of trimethylamine N-oxide (TMAO), a by-product of harmful gut bacteria. High TMAO levels are associated with an increased risk of heart attacks and strokes.
  • Smoking can increase the amount of potentially harmful microorganisms in the gut and decrease the level of beneficial ones. 
  • Certain drugs, such as antibiotics can indiscriminately kill the gut's good bacteria along with the bad ones. Doctors know the harm antibiotics can do so now should only be prescribing them if they think it’s strictly necessary and their use is going to have an overall benefit. It has been estimated that about 24% of drugs inhibited the growth of at least one strain of good bacteria.

Woman in bed stretching

  • Stress and insufficient sleep; about seven hours of sleep a night is a minimum for most.
  • Using too many chemicals, especially disinfectants around the house. Infants may be particularly prone to their effect on the gut.
  • Emulsifiers and artificial sweeteners in foods. It is believed that the latter can lead to an increase in the number of some bacterial strains that are linked with metabolic diseases (a group of conditions that increase the risk of type 2 diabetes and heart disease) and can generally affect the metabolism of glucose in foods
  • An attack of food poisoning or gastroenteritis or any other cause of diarrhoea, which may flush out the colon and deplete beneficial bacterial species
  • Inactivity can compound stress but also contribute to poor gut health.
  •  Having certain illnesses; this includes metabolic diseases such as diabetes.
  • General ageing can cause the gut to carry less of the beneficial bacteria, which is why during this time it is particularly important to pay attention to gut health

How to restore the microbiome to a healthy balance

Let's look at nine ways we can help gain a healthy gut microbiome. 

1. Eat a varied diet

The good bacteria love diversity. This means not eating the same foods day after day but try and be adventurous with your food, eating foods and dishes you’ve never tried before. 

2. Be more plant-based

Eat less meat but more plant-based protein or fish. A more plant-based diet is likely to be higher in fibre and also phytochemicals which the good bacteria thrive on. 

3. Balance your diet 

Eat a balanced diet with the right proportion of carbs (about 45-55% of your diet), fats (about 30-35% of your diet) and protein (about 15%-25% of your diet)

4. Up your fibre intake 

Eat at least 30g fibre a day. Fibre is food to the microbiome and will encourage their growth in numbers and diversity. This can be achieved by eating wholegrain carbs where possible, nuts, seeds, fruit and potatoes with skins on. 

5. Keep active

Research has shown the good bacteria increases with the more exercise you do.

Selection of fermented foods in jars

6. Choose prebiotics and probiotics

Eat probiotics daily such as ‘live/bio yoghurts or yoghurt ‘shot’ drinks. It is still not certain which probiotics are best for particular problems, so daily have at least one probiotic yoghurt or shot drink and a broad-spectrum probiotic supplement.

Eat some prebiotics daily either as food or from a supplement. Prebiotics are a type of fibre and they ‘feed’ the good bacteria, helping their numbers to grow and thus keeping down the numbers of the harmful bacteria. Prebiotics are believed to also help the probiotics tolerate the environment in the gut better, such as the acidity and temperature, and thus be more viable.

Prebiotic rich foods include:

  • asparagus
  • bananas
  • chicory
  • garlic
  • Jerusalem artichoke
  • onions,
  • whole grains

A high fibre diet will generally be high in prebiotics. Cutting down on carbs is not advisable from a gut health point of view.

7. Eat fermented 

Eat fermented foods or drink on a regular basis. These are a natural source of probiotics and include fermented vegetables such as sauerkraut, kefir, kimchi, kombucha, miso, tempeh.

8. Explore polyphenols

Polyphenols are beneficial plant compounds with antioxidant properties and seem to boost the health effects of the intestinal microbiota.

Examples of polyphenols include red wine, cocoa powder and dark chocolate, fruits, especially berries, nuts, beans, vegetables, soya.

9. Consider vitamin D

Have sufficient vitamin D as a supplement (at least 10 mcg) during October to March or throughout the year if you don’t go outside much.


Adults and children who have a compromised immune system problem or are seriously ill should not take probiotics. If in doubt ask the advice of a pharmacist or your GP.

The views expressed in this article are those of the author. All articles published on Nutritionist Resource are reviewed by our editorial team.

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