How to Get Rid of Bad Gut Bacteria

If you’ve been suffering the symptoms of dysbiosis you’re no doubt dying to know how to get rid of bad gut bacteria! Here Hannah, one of our nutritional scientists, breaks down 12 natural ways to kick those pesky bugs to the curb!

Gut health, specifically ridding yourself of bad gut bacteria, is an area of science gripping the health industry.  I don’t think I’ve been this excited about advancements in science since the genetic code was sequenced.

With all the discussion on worst foods for gut health, reducing inflammation, and healing your gut naturally, how do you separate fact from fiction?

I first became interested in gut health when we adopted our second child. Autoimmune disease ran through his birth family, killing his birth grandmother in her 30s.  The pregnancy months were unknown to us, he was born via c-section, was of low birth weight, and had to be on antibiotics for the first 10 days of his life.

Not only that, but, being adopted, we were unable to fully breastfeed him.

As a nutritionist, I conceptually understood the importance of gut health, but it wasn’t until his birth that I really invested time into turning our diet around.

Here’s why…

Your Gut Bacteria and Your Health

Close up of a woman's stomach

You are more bacteria than you are human.  There is some debate over the exact ratio, as it can vary depending on where samples are taken from (i.e lower bowel versus upper digestive tract).  

But it is estimated that there are somewhere between four to ten times as many bacterial cells in and on your body as there are human cells.

As gross as that probably sounds, these bacteria are a living part of you.  

Your digestive tract (lovingly referred to as your “gut” for the purpose of this article) is one of the main places these bacteria love to take up residence. This colony of bacteria — along with fungi, protozoa, and viruses — is referred to as your “microbiome”.  

It can be helpful to think of your gut and your gut bacteria as a factory. Each bacterial species has its own role to play in how your digestion — and the rest of your body — functions.

Research is showing us that your gut bacteria can be linked to a plethora of conditions, including:

  • inflammation
  • IBS
  • cardiovascular disease
  • gum disease
  • poor immune function

Even brain health can be affected!  Gut health can potentially impact mood, behavior, and memory, at least in part via the vagus nerve.  

Fondly known as the “Gut-Brain Axis”, this has serious implications for managing conditions such as:

  • autism
  • depression
  • anxiety
  • ADD
  • dementia

Related Reading: Top 5 Best Digestive Enzyme Supplements to Fix Leaky Gut

Good vs. Bad Gut Bacteria

There are 150 – 400 different types of bacteria in your gut alone.  However, research is telling us that Western cultures tend to have 15 – 30% less diversity of bacteria compared with non-western communities.  

And this is a big problem.

You see, there are two features which make a healthy gut microbiome.

  1. The ratio of good to bad bacteria.
  2. The diversity of bacteria in your gut.

That means that, in the West, we have roughly one quarter less bacteria species in our gut compared with populations who show lower levels of non-communicable diseases such as heart disease, cancer, and diabetes.


The types of bacteria we house are not great either.  We have fewer “good bacteria” and a greater number of “bad bacteria”.

When your ratio of good to bad bacteria is unhealthy, scientists call it “dysbiosis”.  So, what are some good and bad bacteria that live in your gut?

Types of Good Gut Bacteria

Types of Bad Gut Bacteria

What are the Symptoms of Having Bad Gut Bacteria?

Woman resting with a hot water bottle

The symptoms of having an imbalance of good and bad gut bacteria are varied.  But some of the most common symptoms can include:

The long term consequences of bad gut bacteria, as discussed earlier, range from mood disorders to cancer, inflammation, and bowel conditions.

Don’t Miss This: The Best Microbiome Testing Companies: Gut Testing Made Easy

How To Get Rid of Bad Gut Bacteria: 12 Steps

Luckily, having poor gut bacteria now doesn’t mean that you are stuck with them forever! There are a number of simple dietary and lifestyle changes you can make today that will banish those pesky bugs for good!

1. Reduce Your Intake of Gut-Damaging Foods

Earlier you visualized your gut as a factory with different bacteria working away to produce different results.  

Some good, some not so good.

So, what foods should you be avoiding to make sure only the good bacteria are working in your factory?

  • animal-protein foods: Whilst having a variety of protein sources in your diet contributes to gut bacteria diversity, having a diet high in animal protein (meat, eggs, dairy) is associated with a higher level of bad bacteria, particularly Bacteroides and Alistipes species.
  • high saturated and trans fat foods: This is an area of controversy in the health industry today.  However, the research regarding gut bacteria shows these types of fats help bad bacteria thrive, potentially leading to negative health outcomes.  These fats are found in meat, processed foods (such as cakes and cookies), and dairy products.
  • artificial sweeteners: There is some evidence to suggest that artificial sweeteners increase the quantity of some bad bacteria in your gut.
  • Digestible carbohydrates: Also known as starch and simple sugars, digestible carbohydrates have been given a bit of a hammering of late.  Possibly for good reason. Simple sugars may increase the build-up of bad bacteria in the gut. However, the foods simple sugars are found in can also hold beneficial compounds, so do not treat all simple sugars the same.  For example, simple sugars found in processed foods — cookies, cakes, ice cream, et.c — are problematic and should be avoided. Simple sugars found in yogurt, fruits, and vegetables have beneficial components and should not be treated with fear.  

2. Avoid Misusing Antibiotics

Antibiotics are a marvel of modern medicine.  They have saved countless lives. However, as with any medicine, they have possible side effects, too.  

With antibiotics, a hint to their downside is right in their name.  They kill bacteria. And part of the issue with this is the broad spectrum antibiotics often prescribed by doctors.

Broad spectrum antibiotics are just that — broad in the types of bacteria they kill.  They are typically prescribed when a bacterial infection is suspected but it’s not practical to test for which bacteria is responsible.

This overuse and misuse of antibiotics leads to decreases in both your good and bad bacteria, reducing diversity, and, ultimately, the health of your gut.

To fix this, only take antibiotics if you know your illness is bacterial, not viral.  And be sure your doctor is legitimately concerned that you are not able to fight the bacterial infection on your own.  Always finish your whole course of antibiotics.

When you are on antibiotics, it is extra important to make sure you are following the rest of 1 through 12 in this article!

3. Avoid Bacteria-Harming Chemicals

Man dispensing antibacterial soap onto his hand

Just like antibiotics, antibacterial products are designed to decrease bad bacteria — this time on your skin.  Deodorants, soaps, cleaning products, hand sanitizers, and laundry detergents can all have antibacterial properties.

Some recent studies suggest that these products can be absorbed into your body, affecting your gut microbiome.  

It is important to note that there are only a small number of studies in this space at the moment, most looking at the effect of antibacterial agents on animals.  It may not translate to humans.

However, since research has shown there is no significant difference between plain and anti-bacterial soaps for hygiene, you may wish to switch, just to play it safe.

4. Stop Smoking/Avoid Second-Hand Smoke

If you didn’t already know smoking was bad for you, here is yet further evidence to support a smoke-free environment.

Several studies are emerging that link smoking with decreased bacterial diversity and increased bad bacteria.  The changes seen were similar to those shown in people with obesity and Inflammatory Bowel Disease.

If you do smoke, take steps to quit and have a chat with your family doctor.  Make sure you set up rules in your household that any smokers must do so outside, not in the house or the car.  This can reduce the risk of children and other adults being exposed to second-hand smoke.

5. Increase Your Intake of Fiber-Rich Foods

In contrast to what we saw under foods to avoid, non-digestible carbohydrates are beneficial to gut health.  

These foods are fermented in your gut and are a rich source of food for good gut bacteria. These good bacteria eat fiber-rich foods and produce by-products which keep your gut lining healthy, (among many other functions).

Great examples of fiber-rich foods you can include in your diet are:

  • whole grains
  • fruit and vegetables
  • lentils
  • chickpeas
  • kidney beans
  • black beans
  • oats
  • nuts
  • chia seeds
  • other seeds
  • sweet potatoes

6. Increase Anti-Inflammatory Fat Intake

Fresh vegetables, including healthy-fat-rich avocado

Not all fat is created equal.  That is certainly the case when it comes to the human gut. Whilst I discussed above that saturated and trans fats should be kept to a minimum, there are other fats which are actually beneficial to your gut health.  Omega 3 fatty acids and monounsaturated fats are both beneficial for gut bacteria.

Examples of foods that provide these fats include:

  • nuts and seeds
  • avocado
  • fatty fish (such as salmon and sardines)

7. Increase Anti-Inflammatory Food Intake

While acute inflammation helps you fight off infections and heal injuries, chronic inflammation is dangerous for your long term health.  It is linked to diseases such as:

  • cardiovascular disease
  • cancer
  • depression
  • dementia
  • diabetes

Anti-inflammatory foods seem to alter gut bacteria diversity and composition.   This, in turn, can lead to a healthier immune system and a lowered risk of inflammatory diseases.

Some anti-inflammatory foods to include in your diet are:

  • berries
  • cruciferous vegetables such as cauliflower, broccoli, kale, Brussel sprouts, and spinach
  • green tea
  • Capsicum baccatum / peppers
  • grapes
  • turmeric (via isolated curcumin supplements)
  • dark chocolate (70% cacao or higher)
  • tomatoes

8. Increase Your Fermented Food Intake

When we ferment food, we turn it into a probiotic.  This is a substance which enables the growth and life of good gut bacteria.

You want probiotics because they help good bacteria enter, and get comfy, in your gut.  

There are not a whole heap of probiotic foods which are common in traditional Western diets.  (In fact, this may partially answer why our gut microbiome is less healthy than non-Western cultures!)

However, with increasing travel, trade, and immigration, we are finding that the variety of foods, including probiotic foods, is growing in our local shops.

Probiotic foods include:

  • kefir
  • yogurt (not the super sugary flavored kind, the cultured, thick kind)
  • kimchi
  • sauerkraut
  • tempeh
  • natto
  • miso
  • pickles (in salty brine, not vinegar)

How can you incorporate these foods into your day?  Here are three great options!

Chia Seed Pudding: This was a surprise favorite in our household. Normally, I’m not a fan of this sort of texture, but actually took to chia seed pudding much better than I thought I would! The kids love it.  The trick here is to use kefir or probiotic yogurt for a probiotic effect. You can add different flavors such as:

  • avocado
  • chocolate
  • blueberry
  • oatmeal
  • cranberry
  • banana

Smoothie: Blend up a smoothie using kefir or a probiotic yogurt.  Some of my family’s favorite flavor combinations are:

  • banana and strawberry
  • avocado and cocoa
  • blueberries and spinach

Mix Up Your Standard Lunches and Dinners: Try adding kimchi or sauerkraut to a salad, toasted sandwich, wrap, burger, or stir-fry.

9. Add a Prebiotic Supplement

Brightly colored supplements on a white table

Getting a varied diet high in fiber-rich prebiotic foods can be challenging. Whether you live in an area where fresh food is seasonal and often hard to come by, you are not a competent cook, or you simply don’t have time to integrate a lot of foods into your diet, sometimes prebiotic supplements are the best way to ensure you are getting everything you need.

Family-friendly supplements are a brilliant way of making sure picky eaters are getting adequate nutrients, too.

10. Add a Probiotic Supplement

Let’s face it, fermented foods aren’t everyone’s cup of tea.  Getting little ones to eat these foods is particularly challenging.

Probiotic supplements are a very easy way of getting safe, high doses of probiotics to make sure healthy bacteria are colonizing your gut.

11. Get Regular Exercise

Yet another reason to hit the pavement, gym, boxing bag, or whatever form your exercise takes — exercise is being linked to a healthier gut community.

Whilst the exact mechanism is still being worked out — it is likely that exercise plays an anti-inflammatory role in the body, contributing to healthy gut flora — there is little doubt exercise is effective.

It is important to note that there is potentially a difference between perceived voluntary and involuntary exercise.  If exercise is causing stress, it may actually negatively alter the gut microbiome compared to enjoyed exercise.

So, keep exercising for fun, integrate it easily into your day, and don’t overdo it.

12. Manage Stress

Woman relaxing with a book and a cup of coffee

Emerging evidence shows a two-way relationship between stress/anxiety and your gut microbiome.  The vagal nerve is a bi-directional pathway set up between your brain and your gut, sending signals from the gut to the brain and visa versa.

Studies show changes in bacterial composition of the gut during exam time for students, indicating stress may cause changes in the microbiome.

This is an area with still a lot of research to be done, but the initial findings indicate mental health support may be beneficial in keeping your gut healthy.

Take Home Message

The quality and diversity of bacteria in your gut is linked with your likelihood of developing numerous negative health outcomes, including: cancer, heart disease, autoimmune disease, obesity, gut inflammation, anxiety, memory loss, and depression.

The science suggests that focusing on a gut which has a diverse microbiome with an abundance of good bacteria will be of most benefit to your health and longevity.

You can achieve a diverse and healthy microbiome by eating a diet high in pre- and pro-biotic foods and supplements, avoiding unnecessary use of antibiotics and anti-bacterial products, as well as avoiding smoking and stress, and getting plenty of exercise.

Supplementing with butyrate may help your gut wall get stronger, healthier, and more able to do its job. Read Next: Top 5 Best Butyrate Supplements for Leaky Gut Cure


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