Your gut microbiome is as individual as your fingerprint and is something none of us should ignore if we want to lead a healthier and happier life. 

“It is made up of trillions of microbes that respond to what we feed them,” says Dr Federica Amati, head nutritionist at Zoe, a science and nutrition company. “Gut health is dependent on what we ingest every day.” 

Some of what makes it unique is down to genetics, but only to a limited extent. You can’t change your genes, but by eating foods that are linked to “good” microbes, you can modify your microbiome. 

The benefits can often be felt within days, though Amati does offer a caveat: “You have to keep it up. I use the analogy of a garden. If you have a beautiful garden but you never water it and you never weed it, it’s going to suffer

“In the same way, you need to tend to your microbial garden.”

Eat the wrong foods and the microbiome, your gut health, will start to slide. Here are the worst offenders to watch out for. 

The six worst foods for gut health 

Nutritionist, health coach and clinical lead of the Goodwood wellbeing and health programmes Stephanie Moore is the author of Why Eating Less & Exercising More Makes You Fat and her forthcoming book Eat Your Brain Happy.

Here, she reveals six foods that we should avoid or eat less of to promote good gut health. 

Ultra-processed foods

More than half the UK population’s daily calories now come from ultra-processed foods (UPFs) which typically have more than one ingredient that you would rarely find in your kitchen cupboard, or list additives such as preservatives, sweeteners, and artificial colours and flavours. 

High intake of UPFs can change the gut microbiota and lead to inflammation. The following foods are all bad for gut health: 

  • Sausages
  • Chicken nuggets
  • Mass-produced bread
  • Added sugar breakfast cereals
  • Biscuits
  • Added sugar yogurts
  • Instant soups
  • Ice cream
  • Crisps

“Avoid anything with a long list of ingredients with complicated, chemical-sounding names including fizzy drinks, Pot Noodles, savoury snacks such as Wotsits and processed cheese,” advises Moore. 

Eating large quantities of UPFs is associated with heart disease, type 2 diabetes, irritable bowel syndrome, depression, asthma and cancer. 

 “The biggest issue with ultra-processed foods,” says Moore, “is that they’re nutrient-poor, so people over consume them because the body is looking for nourishment and isn’t getting it from them, so we don’t get the signal to stop eating. They also contain emulsifiers, which disrupt the gut microbiome.” 

Deep-fried foods

“The types of oil used in deep-frying – refined seed oils like sunflower or rapeseed, corn or soy are – are by the nature of the refining process highly damaged,” says Moore, “and they’re very high in omega-6, which can be very disruptive to the gut.

“If you heat and reheat the oil, it creates AGEs, which stands for Advanced Glycation End-products, which are damaging to our gut wall. I’m not suggesting you never eat chips ever again, but you should try to reduce the amount of fried food in your diet and, in between, eat really well to support your gut microbes.”

And it’s not just the usual culprits, like fried chicken and battered sausages, you need to watch out for:  “Krispy Kreme doughnuts are among the worst offenders: lots of sugar, refined carbs and then deep-fried.”

Sugar

“Sugar feeds the undesirable microbes in your gut that then crowd out the good stuff,” says Moore. “It also has zero nutritional benefit – in fact we tend to be in a deficit by the time we’ve digested sugar, because we use up nutrients just to break it down. 

“All sugars are bad for gut health. High-fructose corn syrup, a highly processed product, has been shown to be very disruptive to gut microbial composition.

“Raw (unpasteurised) honey and true maple syrup in small amounts do have some nutritional benefit, but still loads of sugar.”

Artificial sweeteners

Artificial sweeteners encourage the proliferation of pathogenic or “bad” bacteria in the gut. “The gut microbiome tries to break them down, but these sweeteners are made up of man-made chemicals that they don’t know what to do with.

“And in the process of the microbes breaking down the artificial sweeteners, some nasty by-products are given off, which kill off the good microbes.”

According to Zoe, some people are more sensitive to the negative effects of artificial sweeteners than others, depending on their individual gut microbiome.

“Sugar alcohols like xylitol tend to be less disruptive,” Moore adds, “but all artificial sweeteners – from sucralose and aspartame to acesulfame potassium (Ace-K) – should be avoided.”

Protein bars and shakes

Protein supplements used to be the preserve of bodybuilders and athletes, but it has become the norm for people nipping to the gym for an hour to consume a protein bar or protein shake. Nutritionists agree that the vast majority of these are not helpful for gut health. 

“Most protein bars are rubbish,” says Moore. “They’re highly processed and contain additives and artificial sweeteners. If they contain more than five ingredients and sugar in any form (including honey) appears in the top five, they’re a no-no.”

However, Moore does recommend some types of protein powder, “simply because we’re understanding more how important it is to get protein into our bodies. 

“My go-to for most people is a high-quality dehydrated, non-flavoured bone broth powder such as Euphoria Bliss. For plant-based, I recommend Pulsin Hemp Protein. If it’s a single ingredient protein powder, without fancy flavourings and all the other yuck they put in, I believe there is a place for it.”

Alcohol

“As much as I love my red wine,” says Moore, “alcohol is liver toxic, neurotoxic and certainly gut toxic. We know that it kills off good microbes and creates disruption in your gut microbiome.

“It also weakens the gut wall and causes inflammation. Sadly, when it comes to gut health, it’s pretty nasty.”

…And three you should consume with caution

Dairy products

“Some people can’t break down the sugar lactose in dairy,” says Moore. “They just don’t make the right enzymes, and that causes unpleasant digestive problems. However, when you ferment dairy and create kefir or yoghurt, or even a well-matured, traditionally made cheese, the fermenting process makes them much more digestible, and they have some beneficial influence.”

Federica Amati also advises people to experiment with removing dairy from their diet  if they feel like they’re not tolerating it well. “A diet high in calcium is good,” she says, “but it can be harmful for people who are lactose intolerant – which is a high proportion of adults. I wouldn’t recommend drinking milk by the glass, but good-quality yoghurts, kefirs and cheeses seem to have a protective effect against colon cancer.”

Foods high in saturated fats

“Any food that contains an excessive amount of fat is linked with increase in inflammation,” says Amati, “and if you increase inflammation, it leads to a number of problems, such as the overstimulation of the immune system. So eating fatty fried foods is not helpful for lots of reasons, including gut health.”

Saturated fats can also compromise the gut lining, resulting in undesirable pathogens passing from the gut into the bloodstream. 

However, many nutritionists, including Moore, stress that saturated fat is not all bad. “Some foods are excellent for the gut despite being full of saturated fat,” she says, “because they help to clean up pathogens.

“Coconut, for example, contains lauric acid and caprylic acid, both of which are antifungal and anti-yeast, so they can help improve the balance of good and bad microbes in the gut.”

Red meat

The consensus among nutrition experts is that excessive consumption of red meat is bad for gut health. Even comparatively lean cuts of red meat, such as top sirloin and T-bone steaks, are high in saturated fats and should ideally be replaced with lentils, beans, chicken or omega-3-rich fish.

 But Dr Nik Kamperidis, consultant gastroenterologist at London Digestive Centre, can also see its benefits. “Red meat is an excellent source of protein and nutrients, and I don’t believe it should be entirely removed from your diet,” he says. “Of course, if someone eats a ribeye steak three times a week, that’s a lot of fat – it’s not going to serve them well. But I’m more in favour of an all-inclusive diet consumed at reasonable rates than one that excludes certain foods.”

Moore concurs. “If it comes from a healthy animal, red meat can be very beneficial,” she nods. “We need to be careful about completely ruling out foods. Human nutrition is complex and nuanced. It’s not black and white.”


What are the signs of an unhealthy gut?

Bloating and gas

Gut dysbiosis – when you have too many bad bacteria living in your gut – can be the cause of discomfort: “The pathogenic or unfriendly gut microbes feed on your food and over-ferment, causing excess production of methane or hydrogen gas,” Moore explains. “So bloating at the end of the day or shortly after eating, is a sure sign of problems with your gut microbiome.”

Constipation

For Amati, constipation is the clearest indication of an unhappy gut microbiome: “Transit time – which means the time a food takes to travel from your fork to the loo – is a good indicator of how well your gut microbiome is doing.” 

Skin disorders

The exact causes are not fully understood but emerging research shows a link between gut health and skin conditions such as eczema, psoriasis and dandruff. 

Weight fluctuation

Unexpected weight-loss or weight-gain can be linked to an unbalanced gut microbiome, though it may also indicate other serious medical conditions. 

Insomnia

Sleep disturbances are often the result of inflammation. “Our gut microbes are hugely involved in the process of how inflamed our bodies are,” says Moore. “Inflammation has your body on high alert: it’s like it’s on fire – it can’t switch off.” 

Reflux

Acid reflux is another red flag, Amati warns, even though it comes from the stomach rather than the gut. “The oesophageal microbiome and the gut microbiome are connected,” she says. “They communicate with each other.”

What are the potential consequences of neglecting your gut health?

There is a growing amount of research indicating that the lower your gut microbiome diversity, the more likely you are to develop inflammatory bowel disease, coeliac disease, type 2 diabetes, psoriatic arthritis and skin conditions such as eczema. An unhealthy assortment of gut bacteria can also contribute to chronic inflammation, which is believed to be a factor in the development of heart disease and cancer.  

Even the less serious consequences of gut dysbiosis can be debilitating. An imbalance in the microbiota living in our gut can result in fatigue and sleep disturbances. It can also influence our mood and our mental health, contributing to disorders such as anxiety and depression, and has an adverse impact on cognitive function, which includes our ability to make decisions, learn and remember. 

How to improve your gut health with diet

“I always talk about the “three Fs” of good gut health,” says Moore. “Fibre, Ferments and Fasting. If you follow these on a fairly regular basis, you’ll improve your gut microbial diversity and end up with a more robust system that can then cope with the occasional bit of gluten, alcohol, sugar or antibiotics. It’s all about building resilience.”

Fibre

The beneficial microbes in your gut feed on different types of fibre, so eating a diverse range of plant foods – especially high-fibre foods like pulses, lentils, nuts, seeds and whole grains – will give them the fibre they need. They also thrive on polyphenols, the colourful, bitter chemicals found in blueberries and dark, leafy greens.

Ferments

In addition to feeding the existing microbes in your gut, it’s helpful to introduce new beneficial bacteria found in fermented and other probiotic foods, such as sauerkraut, kimchi, kefir and yoghurt. 

Fasting

Your gut lining and gut microbes need a chance to recover and reboot. Make sure you leave a window of at least 12 hours between your last calories of the day and your first calories in the morning. 

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