How to increase the good bacteria in your gut and how to get rid of the bad ones

Bacteria gut health
Trillions of bacteria live throughout our digestive system and come in the form of thousands of different species

Not long ago, gut health was a term that most of us only stumbled across when scanning pots of yoghurt in supermarket fridges. But in recent years, we’ve become obsessed.

Fermented foods such as kefir, kombucha and sauerkraut are the new diet stars, there are nine different brands of gut shots available across major supermarkets – a space formerly reserved solely for Yakult – and tens of thousands have sent stool samples to the personalised nutrition company Zoe for microbiome analysis.

All of this is in pursuit of the fuzzy notion of “good gut health” – the idea that we can nurture the bacteria in our intestines for better digestive health but also to ward off serious illness.

What good bacteria are in my gut and how can I get more of them?

Trillions of bacteria live throughout our digestive system, mainly in the large intestine, and come in the form of thousands of different species. This community is referred to as the microbiome. A healthy gut will house a complex mixture of bacteria, while an unhealthy one will be much less diverse.

“A useful analogy is a plain field compared to a lush tropical rainforest,” says Dr Gwo-tzer Ho, a consultant gastroenterologist at the University of Edinburgh.

Among the many microbes that benefit our health are those that produce butyrate – a short-chain fatty acid. “Butyrate has anti-inflammatory properties and is the major energy source for the colonocytes (the cells lining the colon) and therefore helps to maintain gut barrier function,” says Dr Sylvia Duncan, a senior research fellow at the University of Aberdeen’s Rowett Institute. “This helps to prevent bacterial cells crossing this barrier and entering the bloodstream.”

Faecalibacterium prausnitzii is one of these butyrate-producing bacteria, notes Professor Tim Spector, a genetic epidemiologist at King’s College London and the gut expert who co-founded Zoe.

Almost everyone (99.7 per cent of people, studies suggest) houses this strain, which looks like a rod when viewed under the microscope, but concentrations of it vary dramatically between people. Scientists have spotted that sufferers of inflammatory bowel disease, irritable bowel syndrome and bowel cancer tend to have much lower concentrations. High-fibre foods, such as fruit, wholegrains, nuts and dark chocolate, can help it thrive.

Clostridium butyricum, Eubacterium rectale and Roseburia are other bugs that make butyrate. Studies have shown that following a Mediterranean diet can increase the number present in the gut, while Roseburia responds especially well to walnuts and almonds.

Additionally, Clostridium butyricum has been shown to reduce colitis (inflammation of the bowel) and has been linked to a lower risk of colorectal cancer, according to Dr Bunmi Omorotionmwan, a lecturer in microbiology at Nottingham Trent University who has extensively researched gut bacteria. “It can naturally be found in foods like vegetables and sour milk,” she says.

Y-shaped bacteria called Bifidobacteria can also be spotted throughout our digestive system. These bugs digest fibre, help fight-off infections and produce B vitamins and healthy fatty acids. “A lot of credible research shows the Mediterranean diet, including plant foods, nuts and healthy oils, increase these beneficial bacteria,” says Dr Jens Walter, a professor of ecology, food and the microbiome at University College Cork in Ireland.

All of these bugs promote a healthy microbiome and eating plenty of fibre is the key to having a bountiful supply, as bacteria eat these up to produce other compounds that benefit gut health, says Dr Duncan. Fibre also bulks out stools, which reduces constipation and helps remove toxins from the gut, she notes.

“The type of bacteria we have in our gut is heavily determined by what we eat so consuming a balanced diet including fibre-rich foods and vegetables will contribute to a healthy gut,” Dr Omorotionmwan agrees. “Embracing a rich variety of foods is always a good idea to achieve diversity of microbes in the gut.”

However, Dr Ho notes that it’s not all about what we eat. “Data shows that lifestyle factors like avoiding stress, getting good sleep, taking time in eating, holistic wellbeing measures like ensuring a social environment during mealtimes, eating regularly and exercise will all contribute to good gut health,” he adds.

What are bad bacteria and how can I get rid of them?

While the vast majority of the bugs in our intestines benefit our health, some can make us severely unwell.

Clostridium difficile is one example. This bug can set up shop in our intestines without causing harm as our good bacteria suppress it. However, taking antibiotics disrupts this delicate balance and spurs on its growth. This can result in a Clostridium difficile infection, which causes diarrhoea, a fever and nausea. Older people are especially at risk, as the microbiome becomes less diverse with age, Dr Ho explains.

Increasing the number of good bacteria in the gut can prevent these bad bugs from establishing colonies within us and causing disease, says Dr Omorotionmwan.

Bilophila wadsworthia, which looks like a microscopic grain of rice, can also cause problems. Around six in 10 people have it in their gut and it forms part of the healthy microbiome when levels are low. However, eating lots of food high in saturated fat, such as fatty cuts of meat, cheese and chocolate, can increase levels, which triggers inflammation, says Dr Walter.

But this is easily counteracted by cutting back on these foods. “If you eat a healthy diet, your microbiome produces metabolites that are health-promoting and if you eat a not-so-good diet – especially Western diets which tend to be high in fat and sugar – your gut microbiome produces metabolites that are really detrimental,” he says.

For example, eating a very refined diet that is low in fibre causes the microbiome to turn against the gut’s mucous layer, lowering the body’s defences against harmful bacteria, he explains.

Ultimately, a healthy diet is key. “Eat a lot of plant based foods, dietary fibre and healthy fats and avoid saturated fat and processed foods, specifically processed meat,” Dr Walter adds.

What are the signs of good and bad gut health?

Having a diverse range of good bacteria in the microbiome is needed for good gut health, Prof Spector notes. But how do you know what shape your microbes are in? There are some simple ways to check.

“A sign of good gut health is the ability to eat normal amounts of food without getting distressing symptoms,” he notes. Having good energy levels and sleep quality are also markers of a strong microbiome, adds Dr Ho.

“Digestive discomfort or irregular bowel movements may indicate that your gut is not functioning optimally, but gut health influences overall health in many ways, so the signs of poor gut health can vary,” Prof Spector says.

Some less obvious signs of poor gut health include unintentional weight loss and lightheadedness, which signals that a lack of nutrients are being absorbed; regular infections, as much of the immune system is rooted in the gut; and anxiety or depression, as there are links between the gut and mental health, he adds.

Is it worth getting a test or taking probiotics?

Dozens of companies now offer gut microbiome testing. It typically involves collecting a stool sample in a container, sending it off to a lab and waiting for scientists to report back on what bacteria they find.

Zoe is one of the most popular options. Prof Spector says customers receive a breakdown of how many of 50 “good” bacteria and 50 “bad” bacteria their sample contains, along with a microbiome “score”.

“Someone who has a greater proportion of ‘good’ compared with ‘bad’ species is likely to have better markers of metabolic health [such as blood sugar, blood pressure and cholesterol levels] than someone with proportions in the opposite direction,” he says. “Understanding the state of your gut microbiome can be a great way to motivate you to eat a healthy, diverse diet.”

However, the charity Guts UK notes that, while microbiome testing can be interesting, such tests don’t provide a full picture of how healthy the gut is, they won’t pick up all the bacteria in a person’s microbiome and that individual results will vary from sample to sample.

“I would make the argument that you don’t really need advice from these companies,” says Dr Walter. “If you eat a healthy diet you are very likely to benefit from it, independent of how your microbiome looks. So I’m probably more a proponent of just recommending people to eat healthily.”

Other options touted for better gut health include probiotics – live bacteria and yeasts taken as supplements or added to yoghurts that aim to restore a healthy balance of bacteria in the gut. However, as they are technically classed as a food, they are not regulated.

“I do not think there is good evidence that taking probiotics keeps you generally healthier or contributes to disease prevention,” says Dr Walter. “I think there is some good evidence for targeted use of probiotics for irritable bowel syndrome or certain infections.

“It is extremely difficult to select the right probiotics, even for us experts, because it’s the Wild West and it’s really hard to get reliable scientific information on which probiotic to use.”

Dr Ho adds that probiotics are “not a panacea” and that it is difficult to change the gut bacterial populations using them in the long term.

Five ways to reboot your gut health, from Professor Tim Spector

Eat a variety of plants

Aim to eat 30 different plants each week. This includes fruits, vegetables, pulses, herbs, spices, nuts and seeds. Plants are rich in fibre, which is food for your gut microbiome. However, there are many forms of fibre, and different species prefer different forms, so eating a range of plants is important.”

Eat the rainbow

More colourful plants tend to have more polyphenols. These plant compounds are like rocket fuel for your gut bacteria.

Try fermented foods

Fermented foods contain live cultures, which can support your gut health. Fermented foods include live yoghurt, some cheeses, kimchi, kombucha, kefir and sauerkraut.

Fermented foods like kimchi can support your gut health - Getty

Let your gut rest

Try to avoid eating too late at night to allow for a longer overnight fasting period. Certain species of gut bacteria come out at night to “clean up” to allow your gut to recover and work optimally. If you eat too close to bedtime, these microbes don’t have a chance to complete their work.

Limit ultra-processed foods

These foods tend to be high in unhealthy fats, sugar and artificial sweeteners, which don’t support a healthy gut microbiome. They’re also low in fibre and other nutrients your gut bacteria need to thrive.


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