How To Get Rid Of Bad Bacteria In The Gut

Get Rid Of Bad Bacteria in gut featured image

If you’ve been asking yourself, “How do I get rid of bacteria from my gut?” then you’ve been asking yourself the wrong question. 

The proper question you should be asking yourself is, “How do I get rid of bad bacteria from my gut”

Bacteria in the gut are essential for your gut health and overall physical and mental health as they assist in the breakdown of your foods into the vital nutrients your body needs.

Your gut is filled with over 200 different types of bacteria, fungi, and viruses that make up what is known as your microbiome. Many of these bacteria are beneficial, also known as commensal bacteria and we want to support and nurture these bacteria with our diet and lifestyle choices.

While many of these bacteria are beneficial, some can be detrimental to your health. It's important to remove, or minimize these harmful bacteria in the gut to maintain a healthy balance.

Key Takeaways

  • A balanced microbiome is key to gut health.
  • Dietary and lifestyle changes are often effective in managing gut bacteria.
  • Advanced stool testing may be necessary to identify bacterial imbalances and help determine the best treatment plan.

Understanding Bad Bacteria and Dysbiosis

Dysbiosis occurs when there’s an imbalance in your gut microbiome, specifically when harmful bacteria outweigh the beneficial ones. 

This imbalance can lead to a variety of symptoms that affect both your physical and mental well-being, such as bad breath, upset stomach, nausea, constipation, diarrhea, bloating, fatigue, skin issues and even anxiety or brain fog.

To better understand this, let’s break down the types of bacteria in your gut:

  • Beneficial Bacteria: These are the good guys that help with everything from digestion to strengthening your immune system.
  • Commensal Bacteria: Typically harmless and even beneficial at normal levels, these bacteria can become problematic if their populations grow excessively.
  • Pathogenic Bacteria: These are the harmful bacteria that should ideally be absent from your gut, as they are often directly linked to illness and severe health disruptions.

Gut Zoomer 3.0 Test

If you’re experiencing symptoms that may suggest a bacterial imbalance, the Gut Zoomer 3.0 Test can be a valuable tool.

This comprehensive test provides a detailed analysis of your digestive health, the results help to understand if you should be focusing on addressing pathogens or building up the beneficial bacteria levels.

Ways to Get Rid of Bad Bacteria in The Gut

Successfully managing bad bacteria without harming beneficial ones is key to maintaining optimal gut health. There are various natural and herbal remedies that can help restore your gut health effectively.

Implementing a gut health reset involves creating conditions that promote the growth of beneficial bacteria and inhibit harmful ones.

This balance is essential for overall health and can be influenced significantly by your diet and lifestyle choices.

Research has shown that individuals with chronic conditions often have less diversity in their gut microbiome and an excess of harmful bacteria. 

There is a link between microbiome diversity and conditions like Crohn's disease and Irritable Bowel Syndrome (IBS), plus other conditions not commonly associated with gut health like Rheumatoid arthritis and other autoimmune conditions, eczema and even cardiovascular disease.

Ways To Get Rid Of Bad Bacteria

Natural Strategies for Reducing Bad Bacteria 

  • Dietary Adjustments: Emphasize a diverse diet rich in fibers, probiotics, and prebiotics to support good bacteria.
  • Herbal Remedies: Herbal medicines can be specifically tailored to target and reduce populations of harmful bacteria without the collateral damage often associated with antibiotics.
  • Lifestyle Modifications: Regular exercise, sufficient sleep, and effective stress management are all crucial for maintaining a healthy microbiome.

Let’s look in more detail about how to create a healthy gut microbiome to prevent dysbiosis and the overgrowth of bad bacteria.

What You Need To Create A Healthy Gut Microbiome

Following these steps to create a healthy microbiome within your gut will result in the elimination or decrease of bad bacteria. 

The best ways to promote the growth of beneficial bacteria are as follows:

Diet For A Better Gut Microbiome

Optimizing your diet is the most effective way to support a healthy microbiome.

  • Dietary Fiber: Consuming a high-fiber diet from fruits, vegetables, legumes, and whole grains encourages the growth of beneficial gut bacteria. Fiber acts as a prebiotic, providing food for good bacteria and promoting a balanced microbiome.
  • Fiber Supplements: I recommend starting with a FODMAP friendly fiber like Partially Hydrolyzed Guar Gum which is also known as PHGG or Sunfiber, other good fiber supplements include inulin, Galatooligosaccharides (GOS), and Arabinogalactans
  • Fermented Foods: Incorporate probiotic-rich foods like yogurt, kefir, sauerkraut, and kombucha into your diet. These contain live beneficial bacteria that enhance gut health and combat dysbiosis.
  • Reduce Processed Foods: High amounts of processed and sugary foods can disrupt your gut balance, increasing harmful bacteria and yeasts which leads to dysbiosis. Focus on whole, nutrient-dense foods to maintain a healthier gut environment.
diet Healthy Gut Microbiome

Lifestyle Is Important

Your daily habits play a significant role in the health of your gut microbiome.

  • Stress Management: Stress impacts your gut health due to the gut-brain connection. Activities like physical exercise, yoga, or meditation can effectively reduce stress and improve your gut health.
  • Nerva App: This is a hypnosis program focused on the gut-brain balance and I have seen excellent results with clients who have used this program in conjunction with their supplements and diet changes.
  • Sleep: Adequate sleep is crucial for maintaining gut health. Disrupted sleep patterns can upset your microbiome and increase inflammation in the gut. Aim for 7 to 9 hours of quality sleep each night to support a healthy microbial balance.
  • Hydration: Staying well-hydrated aids digestion and prevents the overgrowth of harmful bacteria. Water helps support overall digestive health, and is one of the best treatments for constipation.

Additional Tips

  • Avoid Antibiotics Unless Necessary: While sometimes essential for treating infections, antibiotics can significantly disrupt your microbiome. Use natural remedies and consult with a healthcare professional before turning to antibiotics.
  • Regular Exercise: Physical activity can enhance your microbiome diversity and resilience. Regular exercise not only helps manage weight but also reduces inflammation, both of which benefit gut health.
  • Mindful Eating: Eating slowly and mindfully can improve your digestion and absorption of nutrients, further supporting your microbiome.

Negative Influences

Understanding what harms the gut microbiome is another factor for maintaining gut health. Here are some common negative influences and how you can reduce their effects:


While antibiotics are crucial for treating some bacterial infections, their indiscriminate use can disrupt the natural balance of the gut microbiome, leading to dysbiosis.

This disruption can diminish the diversity and functionality of gut bacteria, making you more susceptible to gastrointestinal disturbances and infections.

  • Use antibiotics only when absolutely necessary, there are often better ways of treating a UTI or sinus infection without antibiotics
  • After a course of antibiotics, consider a diet rich in probiotics and prebiotics to help restore gut health after antibiotics.
Antibiotics Negative Influences

Alcohol and Smoking

Both excessive alcohol consumption and smoking are detrimental to gut health. Alcohol can alter the composition of the gut microbiome and damage the gut lining, leading to increased permeability (often referred to as "leaky gut"). 

Smoking, on the other hand, has been linked to an increased risk of gastrointestinal diseases and can exacerbate conditions like Crohn's disease. There is no safe level of smoking!!

Physical Activity

Lack of physical activity can lead to poor gut health. Regular exercise, however, can enhance gut motility, reduce symptoms of constipation, and positively influence the composition and function of the gut microbiome.

Aim for at least 30 minutes of exercise a day, even going for a walk is beneficial.

Utilizing SelfDecode to Manage Gut Health

SelfDecode provides a personalized approach to understanding your genetic makeup with respect to gut health and other related health aspects. Using SelfDecode you can gain insights into how your genetics may predispose you to gut health issues and how you can effectively manage these risks.

Features of SelfDecode

  • Polygenic Risk Score: This score combines multiple genetic markers to estimate your risk for developing specific health conditions, including those affecting the gut. 
  • Personalized Reports: Receive detailed reports covering various health aspects such as gut health, brain function, and immune system. Each report is tailored to your unique genetic profile.
  • There are reports on IBS, diarrhea, constipation, gluten sensitivity, celiac disease, bloating, leaky gut, H.pylori to name a few of the reports with a gut health focus.
  • Actionable Recommendations: Based on your genetic analysis, SelfDecode provides personalized recommendations designed to improve your health outcomes. These might include dietary suggestions, lifestyle changes, and potentially beneficial supplements.

Benefits of Genetic Insights in Managing Gut Health

By understanding your genetic predisposition, you can take proactive steps to mitigate the risks of developing severe gut conditions. This can include:

  • Tailoring your diet to support the health of your gut lining and reduce inflammation.
  • Choosing probiotics and prebiotics that are more likely to benefit your specific gut flora.
  • Monitoring and adjusting lifestyle factors such as stress and exercise based on your genetic sensitivity.
  • A high genetic risk for a certain condition does not mean that it is going to happen or if it does that you can’t do anything about it!


Maintaining a healthy gut microbiome is less about eliminating all bacteria and more about creating a balance between the beneficial and harmful ones.

By focusing on a diet rich in fibers and probiotics, managing stress, ensuring adequate sleep, staying hydrated, and exercising regularly, you can nurture a thriving gut environment that bolsters overall health and wellbeing.

While lifestyle and dietary adjustments are fundamental, it's crucial to recognize when additional steps may be necessary. 

Advanced stool testing with the Gut Zoomer or the GI Map test can provide a detailed understanding of your gut microbiome, helping to identify specific imbalances that might not be addressed by general wellness strategies alone. 

This targeted approach allows for more personalized and effective interventions.

Remember, it’s essential to consult with a healthcare provider for personalized advice tailored to your specific situatio. For expert guidance on interpreting stool test results and integrating them into a comprehensive health plan, you can schedule consultation with Planet Naturopath.


What is the fastest way to fix Bad gut bacteria?

To quickly improve gut bacteria, focus on your diet by increasing your intake of whole foods and plant-based ingredients. Such dietary adjustments promote beneficial gut flora and enhance overall gut health.

Also, maintaining regular physical activity, ensuring adequate sleep, and managing stress levels can significantly contribute to a balanced gut microbiome.

These lifestyle changes collectively create an environment that supports the growth and maintenance of healthy gut bacteria.

Does fasting get rid of Bad gut bacteria?

Intermittent fasting can positively affect gut health by promoting the diversity and functionality of the microbiome. This eating pattern, which alternates between periods of eating and fasting, may help reset gut bacteria, leading to improved metabolism and reduced inflammation.

Research indicates that such fasting regimens can enhance the resilience and balance of the gut microbiota, thereby supporting digestive health and overall well-being.

*just be careful of too much fasting as too much can be harmful.

Are eggs bad for gut health?

Eggs are generally beneficial for gut health when included as part of a varied diet. They provide essential nutrients that support the digestive system and are easily digestible, making them a good option for people experiencing digestive distress.

Contrary to being harmful, eggs can actually aid in maintaining a healthy gut by providing a source of protein that is less taxing on the gut compared to denser protein sources like meats and legumes.

*however, some people can have a sensitivity to eggs, you can determine this with the Vibrant Wellness food sensitivity test

Recommended Tests

At Planet Naturopath we offer a wide range of functional medicine testing to help you get to the root cause of your health concerns, or simply help you optimize your health.

 All Tests Available page for the full list of available testing options.

Gut Zoomer

If you are wanting to know whether you need to focus on eliminating bad bacteria or building up the beneficial bacteria levels the Gut Zoomer test is going to help by assessing these levels.

Wheat Zoomer

A lot of people can have leaky gut which can trigger many symptoms, the Wheat Zoomer test is not only an advanced wheat allergy and sensitivity test but it also has a detailed analysis of leaky gut.

Food Sensitivity Test

Sometimes it is hard to work out which foods you are reacting to just by eliminating them. The food sensitivity test helps to take out the guesswork and assess if you are reacting to foods or food additives.

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