Burning question: How does your diet affect your gut bacteria?



Question: How does your diet affect your gut bacteria? Are there certain foods you should eat and others you should avoid to keep your gut bacteria healthy?

Gut bacteria has become big business in recent years — in research labs and on supermarket shelves.

We hear much about the powerful effect these tiny microbes have on our health and wellbeing, and are likely to hear more.

That’s because our gut microbiome (or combination of gut bacteria), apart from aiding digestion, is closely linked to our immune system. It’s thought to play a role in conditions like Parkinson’s diseases, heart disease, cancer, multiple sclerosis, autism, asthma, allergies, arthritis, depression and diabetes.

“We’ve got lots of bacteria in our gastrointestinal tracts … And they have lots of jobs in terms of keeping us healthy,” said Dr Emma Beckett, molecular nutritionist at the University of Newcastle.

Our gut bacteria help to produce micronutrients (like vitamins and antioxidants) from the food we eat, as well as break down macronutrients (carbohydrates, proteins and fats) to ease digestion.

“They’re also very important in maintaining the colon wall, helping with its barrier function and uptake of nutrients in our gastrointestinal tracts,” she said.

Probiotics and prebiotics

Your gut microbiome is sensitive to environmental exposures (beginning with the bacteria passed on from your mother at birth) and influenced by genetic factors.

It’s also largely shaped by your diet, said Dr Beckett, and this works in two ways.

“The first way is by eating foods that contain bacteria — so foods with probiotics in them,” she said.

Probiotics are live microorganisms, such as bacteria or yeast, similar to those living in our digestive tract. They are found in fermented foods including yoghurt, sauerkraut, kimchi and kombucha tea.

“With fermented food, it’s the bacteria or the yeast or the fungus that does the fermentation. So if you eat a fermented food, it has those bacteria in there,” she said.

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Probiotics help to maintain healthy levels of “good bacteria” in the gut and support our immune defences. They also help to break down foods we might otherwise find difficult to digest.

“So if you’re lactose intolerant, generally you’d have problems drinking milk. But in yoghurt, the lactose has been broken down by bacteria, so that’s helping you digest that component of the dairy product,” she said.

The second way you can improve your microbiome is through prebiotics: non-living organisms found in food that reach the large intestine unaffected by digestion.

Prebiotics are types of dietary fibres and found in foods like legumes, onions, cabbage, garlic, asparagus, oats, barley and beans.

“By having a high-fibre diet, you’re increasing your chance of being exposed to prebiotics.

“But also high-fibre is going to help to slow the absorption of sugar across the gastrointestinal wall. It’s also going to help keep food moving through the gastrointestinal tract,” Dr Beckett said.

Encouraging diversity

The molecular nutritionist said the modern Western diet lacked a great deal of variety, which could lead to a very low diversity of gut bacteria amongst its populations.

“Even people who do eat a good number of servings of fruit and vegetable, they’re generally eating the same fruit and vegetable over and over again.

“If you think about a traditional Japanese diet for example — one of the gold-standard diets — it’s very high in fermented food, very high in vegetables, very high in seasonal variety… and people live long, healthy lives,” Dr Beckett said.

The problem with supplements

But before you head to the chemist looking for probiotic supplements, Dr Beckett warned these normally only contain a single propriety strain of bacteria.

“So if you’re having a particular supplement, you’re upping that good bacteria, but you’re not necessarily doing the same thing you would be with a probiotic and prebiotic diet that would help maintain the variety of bacteria,” she said.

She also said taking probiotic supplements without fuelling your body with nutritious food (full of prebiotics) was essentially useless.

“You can pop as many live bacteria as you want, but if you’re eating bad things that are going to damage the environment that those probiotics live in, they’re not going to survive.

“You need your prebiotics to go with your probiotics, or there’s not much point putting them in there to start with,” Dr Beckett said.

Foods to avoid

So a high-fibre diet and fermented foods are in. But what is out? Well, too much fat and sugar for starters.

“High fat changes the balance of the carbohydrate digesting bacteria, so you become less good at digesting carbohydrates and breaking down energy with your bacteria.”

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Diets containing too much meat are also a potential issue, she said, because they’re likely to be “high in fat” and can often mean the displacement of fruit and vegetables.

The same goes for alcohol — too much of it can induce dysbiosis (a microbial imbalance).

“So alcoholics have very different bacteria profiles to non-alcoholics. But alcohol is a tricky one, because small amounts of alcohol consumed regularly could have beneficial effect.


Aside from making changes to your diet, the best way to improve your gut health is by ensuring you only take antibiotics when absolutely necessary.

Taking antibiotics often, or for a long period of time, can upset the balance of microbes in your gut.

“Unfortunately, we can’t just target the bad bacteria with antibiotics; it’s a systemic effect,” Dr Beckett said.

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“After you’ve had a course of antibiotics for an illness, you need to think about eating well or taking a supplement to replace the good bacteria.”

A healthy balance

Having a healthy balance of gut bacteria relies on having a balanced immune system that’s able to destroy bad bacteria but keep good bacteria in check.

“If we disrupt our normal bacteria through diet, environment exposures or antibiotics, then we can disrupt complex signalling pathways,” she said.

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Good bacteria are necessary for good health — and to protect us from bad bacteria.

“The more good bacteria you have, the harder it is for bad bacteria for colonise. And that’s not just in your gut — that’s on your skin, that’s in your mouth, and that’s in your nose.”


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