14 Tips To Restore Gut Flora In 7 days (Natural And Science-Backed)

Each one of us has around 100 trillion microbes in our guts. Also known as our gut microbiome, our gut flora is a living community that contains bacteria, viruses, yeasts and other microbes.

Until recently, most people thought of bacteria—or ‘germs’—as enemies that needed to be killed, but as scientists discover more and more about our gut flora, we’re slowly realising how important it is to look after it.

We know that our microbiome contributes to our health by making vitamins and fighting infections. It can even help us to activate drugs (Source: NCBI). Anything that disrupts the balance of microbes in our gut has the potential to cause disease.

Unfortunately for our gut bugs, modern life gives them a hammering. Antibiotics kill good bacteria as well as bad, and they don’t share our love of processed foods. Add to that our fear of dirt and our sanitised, sedentary indoor lives and you have an environment very different to the one our microbiomes co-evolved with us in.

The result? A lack of diversity. That means that many of us—although we all have around the same total number of microbes in our guts—have fewer species of them. As each species has different properties and functions linked to different aspects of human health, that’s not ideal.

Is it possible to restore gut balance?

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14 tips to restore gut flora in 7 days (natural and science-backed)
7-day plan to start restoring your gut health
Key takeaways

Learn more about your gut health. Talk to our experts.


14 easy tips to restore healthy gut flora

The best way to restore gut harmony is with a fibre-rich, nutrient-dense diet.

The good news is that you can begin to change your gut flora with your next meal. Research shows that our gut bacteria are very responsive to what we eat and communities begin shifting almost as soon as we change our diets (Source: NCBI).

However, scientists have also found that when significant damage has been done to the gut through repeated courses of antibiotics, some bacterial communities disappear and are unlikely to return (Source: NCBI).

It’s difficult to know whether or not you’ve restored your microbiome because it’s almost impossible to define what a healthy one is. People’s gut flora is so variable across the world and our lifespans. For instance, babies’ guts are usually dominated by bifidobacteria (Source: NCBI). until they start eating solid foods. This lack of diversity—when compared to an adult microbiome—is exactly what they need to get the most out of their specific diet: milk!

One thing research has confirmed time and time again is that diversity is key. The more families of bacteria in your gut, the healthier you’re likely to be.

There are stool tests which can give a window into your gut. These reveal the levels of specific families of bacteria thought by scientists to help or hinder your health, as well as the presence of certain parasites, yeasts and levels of inflammation.

So, while you can’t actually ‘restore’ your gut microbiome, you can definitely make it better. Here’s how:

1. Pile your plate with polyphenol-rich foods

Polyphenols are compounds found in plant foods that aren’t fully absorbed in our small intestine. That means they become food for the microbes in our colon (Source: NCBI), who transform them into substances with prebiotic, anti-inflammatory, anti-oxidative, anti-carcinogenic, and anti-microbial properties (Source: NCBI).

2. Get a regular sleep routine

The last five years of research into the microbiome have shown that our gut’s microbial residents have a sleep routine of their own. One study found that the gut flora of people with jet lag showed higher numbers of bacteria associated with obesity and metabolic disease (Source: NCBI). Other studies have found that a diverse gut microbiome promotes healthier sleep (Source: PLOS).

3. Ditch the standard Western diet

The evidence for the devastating effect of a processed, high-sugar, low-fibre modern diet on our health continues to mount up. A recent study described our 21st-century diets as “an evolutionarily unique selection ground for microbes that can promote diverse forms of inflammatory disease” (Source: NCBI). This means that the bad bacteria in our guts appear to love our deficient diets, while the all-important good ones aren’t so keen.

4. Get some exercise, but not too much

The science on this has really sped up over the last decade. We now know that exercise has a direct effect on our gut bacteria, who in turn improve our tissue metabolism, cardiorespiratory fitness, and insulin resistance (Source: NCBI). However, our bodies perceive too much heavy exercise as a threat, which invokes the stress response, thus reducing our gut flora diversity (Source: NCBI).

5. Double your fibre intake

Fibre isn’t really food for us at all: unlike horses, elephants or cows, we can’t extract any nutrients from it. But our gut flora thrive on it. The research to back the benefits of a high-fibre diet is overwhelming. One study found that a low-fibre diet can trigger a substantial dip in the diversity of our gut flora, increasing the risk of metabolic syndrome and obesity-related disease, Crohn’s disease, ulcerative colitis liver, disease, and colorectal cancer (Source: NCBI).

6. Ban added sugar from your life

Added sugar is like rocket fuel for your microbiome. That sounds like a good thing, but unfortunately it appears to encourage specific families of bacteria to ‘take over’, crowd others out and tip a balanced gut into dysbiosis. In one study, mice fed high-sugar diets lost gut microbial diversity, and developed leakier guts: the tight junctions in their gut walls actually opened wider due to inflammation caused by high sugar intake (Source: NCBI).

7. Get fermenting

Human beings have been fermenting their food and drink for thousands of years. The fermentation process activates immunoglobulins, antibacterial peptides, antimicrobial proteins, oligosaccharides, lipids, and short amino acid sequences (depending on the particular food). Together, these appear to have antioxidant, antihypertensive, antimicrobial, and other bioactive effects (Source: NCBI).

8. Play with your pet

Most of us have been told that we should wash our hands after playing with our furry friends. But it looks like having a pet—and sharing their germs—could actually be great for our microbiomes, reducing the risk of allergies and obesity (Source: NCBI).

9. Get dirty

Studies show that growing up in microbe-rich environments—such as on a farm—can protect children from chronic disease as they get older (Source: NCBI).

10. Chuck out your artificial sweeteners

Artificial sweeteners are bad news. Some studies have found they’re not dangerous, but a recent research paper found that they cause glucose intolerance in some groups of people by altering the gut microbiome (Source: NCBI).

11. Stop cleaning so much (yes, really)

Our hatred of bacteria is big business. We’re offered a never-ending supply of antibacterial cleaning substances to drench ourselves and our houses in. While it’s not sensible to eat your dinner off your dirty kitchen floor, it’s not necessary to disinfect your hands or your work surface every five minutes either.

12. Simplify your life

Isn’t it incredible how an emotion can affect the living things in our bodies? When we’re stressed, our bodies release a cocktail of hormones that prepare us to fight, fly or freeze, which then impacts our microbiome (Source: NCBI). Stress is useful for running away from lions, but disastrous for our gut flora in the long term.

13. Fast

It seems strange that we can help our gut flora by not eating and therefore starving them, but one study in mice found that changes in the microbiome as a result of fasting were associated with increases in gut mucus (a good thing), numbers of goblet cells (the cells that produce mucus) and length of villi (the finger-like structures on the lining of your gut that help to absorb nutrients) (Source: DIABETES JOURNALS). It’s likely fasting has a similar effect in humans.

14. Find out if you have any infections or imbalances and address them

There are many types of worms, parasites and single-celled pathogens that can infect our guts. Sometimes they cause no symptoms, but other times they can cause no end of trouble. For instance, a protozoa called Giardia has been found to have a dramatic effect on our gut flora (Source: NCBI). You can find out more about parasitic infection here.

SIBO is an overgrowth of bacteria in your small intestine (where levels of bacteria should be very low), which can affect the balance of bacteria in your large intestine. If you suspect you have SIBO, you can read more about the symptoms, testing and treatment here.

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7-day plan to start restoring your gut health

‘Start’ is the key word here.

As mentioned before, gut bacteria respond quickly to changes in diet, but a total restoration of your gut flora is a) difficult to define and b) even harder to prove.

Ideally, we should all have the microbiomes of the hunter-gatherer societies our ancestors lived in. It’s likely that’s impossible in the Western world. But don’t despair! We can start to restore healthy bacteria in our guts with a few changes.

Day 1

Start fermenting. Sourdough bread is easier to make than you think and sauerkraut (a traditional German pickled cabbage) gives you the benefits of a fibre- and polyphenol-packed cruciferous vegetable too. Many people say that fermenting their own food is therapeutic, so perhaps restoring gut bacteria can be a good way to relax too!

Day 2

Roast a huge batch of vegetables, keep them in the fridge and eat them over the next few days. Maximum fibre and polyphenol impact, minimum effort. Try roasting cauliflower, broccoli, red onion and beetroot in olive oil.

Day 3

Plant your own vegetables or herbs. OK, you won’t eat them for a while, but even the act of getting our hands in soil is good for our guts.

We know that contact with soil is great for our skin microbiome (yes, your skin has a microbiome too) (Source: NCBI). We also know that contact with the earth and soil was a major factor in the evolution of our ancestors’ gut microbiomes, and research has shown that people living traditional rural lives have more diverse gut flora as a result (Source: NCBI).

Day 4

Replace any white, refined grains in your diet in your cupboards with whole, brown versions. There’s much more fibre in brown rice and whole grain bread and pasta than their white counterparts. If you soak your brown rice for 24 hours before cooking it, it’s easier to digest and the nutrients are more available too (Source: NCBI).

You could try naturally gluten-free whole grains like quinoa, buckwheat, millet or amaranth. Variety is key for gut health. If you can find it, and you can tolerate gluten, brown or rye sourdough bread is great for your gut, because the slow fermentation process uses probiotic bacteria instead of yeast to make the bread rise.

Day 5

Get out in nature. We’ve already learnt that stress is bad for your gut bugs, and one of the most available and effective ways of de-stressing is to simply step outside. A recent study found that visitors to a natural environment reported significantly lower levels of stress—and showed lower levels of the stress hormone cortisol—than their counterparts visiting a more urbanised outdoor setting (Source: NCBI).

Day 6

Try a probiotic supplement. While fermented foods like yoghurt, sauerkraut, sourdough bread and traditionally-made pickles are probiotic foods (good bacteria are used in the fermentation process), probiotics also come in the form of supplements, like pills, powders and liquids. Some of them have been extremely well-researched and have a lot of evidence behind them to prove their positive effects.

Probiotic supplements have been found to ‘remodel’ the gut after a course of antibiotics (Source: NCBI), and ‘Mutaflor’—which contains a beneficial strain of E. coli bacteria—has put people with Ulcerative Colitis into remission (Source: NCBI).

Day 7

Try prebiotics. Not to be confused with probiotics—although they do enjoy each other’s company—prebiotics also come in both food and supplement form.

Prebiotics are food for bacteria because they pass through our small intestines without being digested and end up as food for the bacteria in our large intestine. In the case of prebiotic foods, some parts of that food will be digestible: for instance a banana contains simple sugars that we can digest, and oligosaccharides that we can’t digest (but our bacteria can).

Prebiotic supplements are usually much more powerful than prebiotic foods. Going back to that banana: it typically contains 0.21 grams of fructo-oligosaccharides (FOS), while most supplement manufacturers recommended a starting dose of 5 grams per day. Although studies have found it to help diversify the microbiome (Source: NCBI), lower cholesterol (Source: NCBI) and ease constipation (Source: NCBI), if you have IBS, use FOS with caution as it can worsen diarrhoea and gas (Source: NCBI).

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Learn more about your gut health. Talk to our experts.


Key takeaways

  • While it’s not possible to know if we can completely restore our gut flora—or even what that would mean (what point of our lives or ancestral past are we aiming to restore it to?)—we can certainly help it along.
  • We know that our gut flora changes when our diet changes. Research so far has told us that it can happen quickly.
  • If you want to restore your microbiome, your best bet is to feed it with high-fibre whole foods, establish a good sleep routine, get out in nature and simplify your day-to-day life. Prebiotic and probiotic supplements could really help too.

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Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.

Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.
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