How Long Does It Take To Repopulate The Gut With Good Bacteria?

Everyone seems to be after good bacteria these days. While there’s no doubt that some types of bacteria are better for us than others, taking a random probiotic supplement is unlikely to instantly solve your gut woes.

To find out how to get your beautiful bacteria working for you, read on.


How Do You Repopulate The Gut With Good Bacteria?
How Long Does It Take To Replace The Gut With Good Bacteria Naturally After Antibiotics?
What Are The Symptoms Of An Unhealthy Gut?
How Long Does It Take For Inflamed Intestines To Heal?
How Long Does It Take To Restore Gut Bacteria After Leaky Gut?
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How do you repopulate the gut with good bacteria?

The best way to repopulate your gut with good bacteria is to feed the ones that are there already.

We all have somewhere around 1000 types of bacteria in our guts, making up a community of about 100 trillion microbes. The more types of bacteria you have down there, the lower your risk of disease and allergies. We know this from many animal tests and human studies comparing the microbes of people with and without particular diseases.

Recent examples include:

Modern life does a number on your gut bacteria. Scientists who have lived and worked with traditional hunter gatherer cultures around the world and tested their microbiomes have found that they have a far higher diversity of bacteria than people in developed countries.

The Hadza people of Tanzania have a gut microbiome diversity about 40 per cent higher than the average American and about 30 per cent higher than the average Brit (Source: NCBI).

While probiotics can certainly play a role in restoring a dwindling microbiome, the latest research tells us that their long-term effects are minimal if we don’t eat the right diet to keep them alive. Find out more about probiotics on our blog How long does it take for probiotics to start working?

The average Hadza person eats around 600 species of plants and animals in a year. They have virtually no common Western diseases like obesity, allergies, heart disease and cancer. Shockingly, most Westerners have fewer than 50 species in their diet, and are many times more likely to be chronically ill or obese than the Hadza (Source: NCBI).

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


Destroyers of diversity

Our lifestyles today are stamping out the diversity in our gut microbiomes. Let’s look at how:


It depends on the type of antibiotic, the state of your microbiome to begin with and so many other factors, but repeated courses of antibiotics over your lifetime will almost certainly cause a permanent drop in the diversity of your microbiome (Source: NCBI).


It seems far-fetched, but there’s a lot of evidence now that the stress chemicals our body releases when we’re anxious, afraid or upset affect the bacteria in our gut. Over time, chronic stress takes its toll on our bacterial balance (Source: NCBI).

How Long Does It Take To Repopulate The Gut With Good Bacteria?

Caesarean section

Babies are born with very few bacteria in their guts, and are designed to pick up their first batches from mum’s birth canal. Research shows that babies born by c-section have gut microbiomes more similar to the typical skin microbiome, while those born vaginally have more diversity, and consequently, are less likely to suffer from allergies (Source: PUBMED).

Bottle feeding

Breast milk has evolved over millions of years to contain everything a baby needs, including mum’s bacteria and nutrients to feed that bacteria so it can set up home and multiply in a baby’s gut (Source: PUBMED).

Low-fibre diets

Our gut bacteria love to chow down on fibre. Sadly for them, in the ‘civilised’ world, we no longer do. A typical Western, processed, convenience-food diet is almost devoid of fibre, so it’s bad news for bacteria (Source: PUBMED).

Too much sugar and white carbs

Sugar and refined carbohydrates like white flour, white rice and corn are not only almost completely free of fibre, but of almost any nutrient. They also cause spikes in blood sugar and negatively affect our gut bacteria by over-feeding certain types (usually the types we don’t want to encourage) which then take over and crowd out the types we do want (Source: NCBI).

Being too clean

Time and time again research has shown that the further away we get from nature, the less diverse our microbiomes are likely to be (Source: PUBMED).

Humanity’s gradual move into urban areas has contributed to the increase of allergies and autoimmune disease. Growing up in a ‘dirty’ natural environment decreases the chances of developing allergies (Source: NCBI).

Lack of exercise

Our gut bacteria appear to ‘like’ moderate, regular exercise and flourish when they get it, while a sedentary lifestyle or over-exercising has a negative impact on our microbiomes (Source: PUBMED).

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How long does it take to replace the gut with good bacteria naturally after antibiotics?

Replacing your gut with good bacteria after antibiotics can start right away: you can start looking after your gut health while you’re still taking a course of antibiotics.

While 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), 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).

To get the full lowdown on how to restore your gut flora after antibiotics, check out our blog post 14 tips to restore gut flora after antibiotics.
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Learn more about your gut health. Talk to our experts.


What are the symptoms of an unhealthy gut?

Gut conditions like IBS, constipation, bloating and diarrhoea are all signs of an unhealthy gut (Source: NCBI).

But the health of your gut has far reaching consequences for the rest of your body, and even your mind.

Symptoms like fatigue, anxiety and sleep disturbances (Source: NCBI) can be indications that all might not be well with your gut, as well as more serious conditions like:

It’s important to remember that research has only found links between these diseases and changes in the gut, not causation. Which means that we’re not yet sure what comes first, the gut issues or the disease.
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How long does it take for inflamed intestines to heal?

It’s difficult to say how long it takes for inflamed intestines to heal, because it depends on why they’re inflamed in the first place.

At Healthpath, we’re not doctors. We can’t tell you if your intestines are visibly ‘inflamed’: while inflammation plays a part in IBS symptoms like diarrhoea, bloating and constipation, inflammation that the eye can see (through a special camera) is usually an indication of IBD
(Crohn’s disease or ulcerative colitis). Only a doctor can diagnose you with IBD.

However, IBS symptoms can certainly make it feel like your intestines are inflamed. Finding a long-term solution to diarrhoea, bloating and constipation takes identifying and tackling the root cause. This is where The Healthpath Gut Health Test can help: it gives a window into your gut, revealing the levels of specific types of bacteria that could be helping or hindering your health, as well as the presence of certain parasites, yeasts and levels of inflammation.
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How long does it take to restore gut bacteria after leaky gut?

How long it takes for your leaky gut to get better depends on a few factors. It’s worth saying here that while we know that leaky gut—or intestinal permeability, as scientists call it—definitely exists, and is a potential cause of many diseases (Source: NCBI), it hasn’t been researched very much as a condition in itself.

So while we can’t give you a timescale, we know from experience that people tend to feel better faster if they follow these suggestions:

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Key takeaways

We can’t tell you how long it will take to repopulate your gut with good bacteria, because everyone is different. It depends on:

  • How your gut bacteria became depleted in the first place
  • Whether or not you have any underlying infections or imbalances (this is where a Healthpath Gut Health Test is useful)
  • Your individual biochemistry and genetic predisposition

Perhaps more important than any of these is your lifestyle. If you’re willing to do the following, good gut health may come quicker:

  • Eat a whole-foods, fibre-rich diet
  • Reduce stress
  • Moderate your alcohol intake
  • Give up smoking
  • Prioritise sleep

Get an in-depth insight into your gut

View our gut health tests

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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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