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Illustration of a stomach full of flowers and butterflies

The digestive microbiome: How important are gut microbes for our health?

The microbes in our gut and the genes that control them can influence everything from weight to illness risk to healthy ageing. Patsy Westcott investigates.

Even a decade ago the importance of the microbes – aka the bacteria, fungi, yeasts and other microscopic organisms that inhabit our gut, skin, mouth and so on – was only just starting to be recognised.

Today we bandy around words like microbiota and microbiome as casually as we quaff kefir, cultivate kimchi or slip a bottle of kombucha into our shopping basket to 'feed' those microbes.

But do we really understand this universe within? Is the microbiota the same as the microbiome, how exactly do microbes shape our health, and can we encourage them to help us stay well?

"Microbiota is the word used to describe microbes, while the microbiome is the set of genes – or genome – controlling their action," explains consultant neuro-gastroenterologist, Dr Anton Emmanuel, of University College London.

What is the microbiome?

Just as different plants and animals thrive in different environments, so each habitat on and in our bodies houses its own distinct microbial community. One of the most important of these resides in our gut, which is home to trillions of microbes, including at least 1,000 different species of known bacteria and many more that are currently unknown.

Meanwhile, with more than three million microbial genes, 150 times the number of human genes, it's fair to say we're more microbial than human.

"Your gut microbes are as individual as your fingerprint," explains Dr Emmanuel. Our birth, how we were fed as babies (Caesarean and bottle-fed babies have less varied microbiota), diet, lifestyle, age and where we live are just some factors that shape our unique microbial fingerprint.

Image of gut microbesHumans have more than three million microbial genes, and your gut microbes are as individual as your fingerprint.

Gut microbes and our health

Scientists are still discovering how microbes fit into the bigger picture. Established functions include promoting nutrient absorption, programming our immune system to fight off allergies and infections, determining our response to foods and medications, influencing the illnesses we are susceptible to and even affecting how we age.

"Microbes are a co-factor in conditions from atopic dermatitis (eczema) to inflammatory bowel diseases, such as Crohn's disease and colitis, as well as other diseases in which the immune system turns against itself (autoimmune diseases), such as rheumatoid arthritis and psoriasis," observes Dr Emmanuel. "There's also growing evidence they are involved in nervous system diseases, such as MS and Parkinson's, as well as mood disorders like anxiety and depression," he adds.

The ageing process

One of the newest frontiers in microbial science is ageing. As we age our gut microbiota undergo dramatic changes, which can transform them from allies into foes. Can we reverse this?

It's still largely uncharted territory, but a 2019 Korean study,1 which found that the microbiota of centenarians are rich in health-linked bacteria and low in bacteria associated with disease, suggests it may be possible; perhaps with the aid of age-specific pre- and probiotics or faecal transplants (see below).

Faecal transplants

'Poo' – aka faecal – transplants are another way doctors are harnessing the power of gut bacteria. Mainly performed for treatment of the drug-resistant superbug Clostridium difficile, there's growing interest in their potential to help problems such as obesity and pre-diabetes (aka metabolic syndrome).

The genetic factor

Scientists are beginning to tease out how microbes interact with genes and factors such as what and when we eat and sleep, appetite, hunger and exercise habits. In PREDICT, a groundbreaking series of UK-US studies, researchers discovered to their surprise that even identical twins share just 37 per cent of gut microbes – only slightly higher than the 35 per cent shared between unrelated individuals – and have different reactions to food.2

"We've learnt that the microbiome is a key player in the rise in blood glucose that occurs after a meal and has an even more potent effect on the rise in blood fat," says PREDICT researcher Dr Sarah Berry, senior lecturer in nutritional sciences at King's College London.

Prolonged rises in blood glucose and blood fat over time increase the risk of type 2 diabetes and cardiovascular disease, so these findings could help explain how our microbiota could contribute to these diseases and how, by choosing the right foods for us, we could avoid them.

There's no one-size-fits-all solution, but for now experts agree that the most important thing for our microbes – and for our health – is a varied, fibre-rich diet. "Diversity is more important than specific foods," says Dr Emmanuel.

How can probiotics help?

These insights look set to lead to personalised diets tailored to our individual response to foods. A new high-tech widget and app, developed by Zoe, the company funding the PREDICT science studies, is currently being developed that will enable us to monitor our response to food and tailor our diet accordingly.

We're also likely to see the introduction of personalised probiotics to help prevent and treat disease. Probiotics are already being tested to help restore microbial balance disrupted by illness or cancer treatments such as chemotherapy and radiotherapy. Recent studies, meanwhile, suggest that specific species of gut bacteria could aid new 'biological' cancer therapies targeting the immune system.

Small bowls of different probiotic foodsProbiotic foods such as kefir and sauerkraut are becoming increasingly popular, while probiotics are currently being tested to help restore microbial balance disrupted by illness.

Microbiome diet

How can you foster healthier microbes? Diet is key. A major job of our gut microbes is to ferment fibres found in plant-based foods – leafy green veg, herbs, roots, fruit, nuts and seeds – that have escaped digestion higher up the digestive tract.

This helps fuel the growth of more specialised microbes, which in turn produce compounds needed for a slew of bodily functions including appetite regulation and blood glucose control.

Probiotic foods

There's lots we can do to feed our microbes. Here are some foods to try.

Live bio-yoghurt

The process of fermenting milk to make yogurt boosts 'friendly' bacteria.

Kimchi

Korea's signature dish made from fermented cabbage is as gut-friendly as it is moreish.

Sauerkraut

One of the world's oldest fermented foods, this tangy cabbage pickle contains a wealth of 'friendly' bacteria.

Kombucha

Research suggests this fermented tea can have a favourable effect on the gut microbiota – at least in animals.

Miso

This paste of fermented soya beans, rice or barley popular in Japan has been shown to help boost healthy microbiota.

Patsy Westcott MSc is a freelance writer specialising in health and nutrition, and writes regularly for various print and online publications. She has a Master's degree in Nutritional Medicine and has contributed to more than 40 health and nutrition books.

Nothing beats a healthy, balanced diet to provide all the nutrients we need. But when this isn’t possible, supplements can help. This article isn’t intended to replace medical advice. Please consult your healthcare professional before trying supplements or herbal medicines.