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How to Get Rid of Bad Bacteria in the Gut Naturally: 4 Steps

Written by Dr. Michael Ruscio, DC on August 22, 2025

Written by Dr. Michael Ruscio, DC on August 22, 2025 — Reviewed by Kellie Blake

• Microbiome Imbalance Causes|
• Symptoms|
• How to Get Rid of Bad Bacteria|
• Probiotics|
• Diet|
• Stress Management|
• Antimicrobials|

Reducing harmful bacteria in the gut is a crucial step toward achieving good digestive health and better overall well-being, especially when done as a part of a balanced approach to gut health.

What we often think of as “bad” bacteria aren’t always harmful. In fact, many are neutral or even beneficial when balanced within a diverse microbiome. So, a healthy gut isn’t simply about “good” or “bad” bacteria—it’s about achieving balance among different types. 

The gut microbiome includes a variety of microbes, mainly bacteria, along with some fungi and other organisms. When this ecosystem becomes unbalanced, problematic microbes can take over.

This can contribute to a range of issues throughout the body, including infections, gastrointestinal symptoms, skin conditions, and even mental health problems.

In this article, we’ll explore how to get rid of bad bacteria in the gut with four steps that can support a healthier gut microbiome overall.

What Causes Microbiome Imbalance?

Harmful bacteria can increase when the gut microbiome becomes unbalanced. Various lifestyle and environmental factors can contribute to imbalanced gut microbes—also called dysbiosis:

• Overuse of antibiotics 1—These can wipe out both harmful and beneficial bacteria, leaving the gut vulnerable.
• High stress levels that activate the fight-or-flight response 2—Stress can alter gut motility and reduce beneficial microbes, giving bad ones room to grow.
• Poor diet—Diets high in sugar, refined carbs, and processed foods can feed bad bacteria and yeast.
• Lack of sleep and exercise—Both are critical for a healthy immune system and microbial diversity.

Additionally, many chronic conditions and diseases are linked to gut dysbiosis, including irritable bowel syndrome (IBS) 3, fatty liver disease 4, depression 5 obesity 6.

Over time, these factors can allow harmful microbes to dominate your microbiome, leading to gut health issues and symptoms that can decrease your well-being.

Symptoms of Imbalanced Microbiota

In the clinic, our clients often report symptoms that suggest imbalances in the microbiota. These symptoms include:

• IBS-type symptoms, such as bloating, gas, and belly pain
• Constipation or diarrhea (or both)
• Food sensitivities 
• Autoimmune signs and symptoms (e.g., thyroid antibodies)
• Mental health effects, including anxiety, depression, and brain fog

How to Get Rid of Bad Bacteria in the Gut: 4 Steps

We can think of the microbiome as a delicate ecosystem, like a garden. Basic supports, such as a whole-foods diet, probiotics, and occasional cautious use of antimicrobials, can help it thrive. 

Getting rid of bad bacteria is sometimes necessary—for example, when we need antibiotics to treat an infection. But focusing solely on killing harmful microbes is like applying weed killer without watering or fertilizing. As a result, the plants in the garden (the beneficial gut microbes) will suffer.

Addressing the whole person with good nutrition and other supportive habits is crucial to correcting microbiota imbalances and improving symptoms. 

The four main steps we use to help clients get rid of microbial overgrowths and a generally imbalanced microbiome are:

1. Probiotics
2. A gut-supportive diet
3. Stress management
4. Antimicrobials when necessary

Although they aren’t a quick-fix method, these steps typically help clients feel much better over time. 

It might take a few months for an imbalanced microbiome to recover completely. But symptoms often start to improve within days or weeks, which can help you stay the course.

Step 1: Take Probiotic Supplements

Taking probiotics is one of the most well-supported strategies for improving gut health, especially when the microbiome is imbalanced.

Probiotics can help to crowd out unhealthy bacteria and increase the overall health of the microbiome.

Multi-strain probiotics appear to be especially good at increasing beneficial bacteria numbers and improving symptoms in people with IBD (inflammatory bowel disease) 7.

Probiotics can also be effective for addressing SIBO (small intestinal bacterial overgrowth). A meta-analysis (highest quality study of studies) found that single-strain and multi-strain probiotics got rid of overgrowths in the small intestine in more than half (53%) of SIBO patients 8.

Probiotics can also: 

• Help people with constipation have more regular and comfortable bowel movements 9
• Reduce bloating 10
• Improve IBS symptoms 11
• Promote healthy immune activity in the gut and reduce inflammation in the digestive tract 12
• Reduce damage to the gut lining, also known as leaky gut 12

Research tells us that the more unbalanced the gut microbiota, the greater the benefits probiotics can bring 13. 

In fact, probiotics may have less of an impact on a healthier microbiome 14. That’s good news because it means we probably don’t need to take probiotics forever to maintain gut health.

Choosing the Right Probiotic

Various strains of probiotics can be beneficial for gut health. Any trusted brand offering at least 1 billion CFU per day should be able to restore healthy levels of good bacteria.

However, scientific research and my clinical experience have shown that combining different types of bacteria may work best. We recommend our clients take a blend of Lactobacillus and Bifidobacteria, Saccharomyces boulardii cerevisiae (beneficial yeasts), and a soil-based probiotic together for optimal results.

In our clinic, we typically recommend taking all three categories of probiotics—an approach we call triple therapy. Here’s how we outline our triple-therapy probiotic protocol:

Step 2: Eat a Microbiome-Friendly Diet

Probiotics can support gut health, but their benefits are even greater when combined with a diet that helps rebalance the microbiome. What you eat plays a major role in shaping your gut bacteria—so while probiotics can help restore balance, your diet lays the foundation for long-term gut health.

There’s no one-size-fits-all approach, but in general, a gut-supportive diet should 15:

• Reduce inflammation
• Manage blood sugar
• Minimize food sensitivities and intolerances
• Provide healthy carbohydrates and prebiotic fiber to feed good bacteria

Diets high in diverse plant foods are linked to more microbial diversity and less harmful bacteria 16. But too much fiber—especially insoluble fiber like wheat bran—can aggravate symptoms in some people. Fiber and carbohydrate intake should always be tailored to individual tolerance and gut health status 17.

At the clinic, we commonly recommend three evidence-based diets that support microbiome balance. The best fit depends on your symptoms, sensitivities, and starting point.

A Gentle Start: The Mediterranean Diet

The Mediterranean diet is rich in microbiota-friendly foods like colorful fruits and vegetables (high in polyphenols), legumes, whole grains, fish, and unprocessed proteins.

Research supports its anti-inflammatory effects 18 and ability to enhance microbial diversity 19—making it an excellent first choice for those without fiber-related gut issues or intolerances to dairy or wheat.

A More Focused Approach: A Paleo Diet

A Paleo diet is a whole-foods approach that limits grains and dairy while emphasizing meats, fish, vegetables, fruits, nuts, and seeds. It’s lower in carbohydrates and naturally excludes common triggers like gluten and dairy, which makes it a helpful reset for many.

Though Paleo is not as extensively studied for microbiota health, its anti-inflammatory effects and blood sugar-stabilizing qualities often lead to symptom relief and improved energy 18.

Download: Our Paleo Diet Guide

Targeted Relief for Tough Symptoms: A Low FODMAP Diet

If symptoms persist despite trying the Mediterranean diet or a Paleo diet, a low FODMAP diet may help. It removes specific fermentable carbs (FODMAPs) that can cause gas, bloating, and diarrhea in sensitive individuals.

This diet has strong clinical support for easing IBS and SIBO symptoms—especially when combined with probiotics 20 21. While it may temporarily reduce some beneficial bacteria at first 21, most people tolerate a wide range of other gut-healthy foods on the plan. Over time, FODMAPs should be reintroduced gradually to restore microbial diversity.

Download: Our Low FODMAP Diet Guide

Bonus Support: Add Intermittent Fasting

Combining any of these diets with intermittent fasting may accelerate gut repair. Time-restricted eating (like eating within an 8–10 hour window and fasting overnight) gives the digestive system time to rest and may support microbiome balance 22 and improve metabolic health 23.

Step 3: Manage Stress to Support Your Gut Microbiome

Chronic stress can disrupt the balance of your gut microbiome. That’s because stress hormones—like cortisol and adrenaline—may affect how gut bacteria behave and how well your digestive system works 2. Regular movement, time in nature, and quality sleep can all help reduce stress and support gut health.

Exercise

Exercise is a key way to manage stress, but it may also support gut health by:

• Promoting a more diverse microbiota 24
• Encouraging healthy bacteria to produce short-chain fatty acids (SCFAs), which reduce inflammation and support immune function 25
• Supporting proteins called toll-like receptors (TLRs) that help the gut’s immune system and lower inflammation 26 27

Doing moderate-to-high-intensity exercise (like cardio or strength training) for 30–90 minutes three times per week can positively impact the microbiome 24.

But listening to your body is key: Both over- and under-exercising can stress the gut. For those just starting, walking daily is an excellent foundation to build upon. As fitness levels improve, adding more intense or varied workouts can enhance these benefits.

Mind-Body Practices and Time in Nature

Stress management practices like meditation and mindfulness can reduce inflammation and encourage a healthier gut environment 2. 

Spending time outdoors is also highly beneficial. Research suggests that natural settings can reduce perceived stress, balance the autonomic (involuntary) nervous system, and lower cortisol and blood pressure 28 29. 

Walking in nature may be even better than walking in urban areas because both movement and nature can relieve stress. Studies show that walking in nature combines the benefits of physical activity and natural stress reduction, further enhancing gut health and overall health 30. 

And if getting outdoors isn’t always possible, even looking at images of nature (like a screen saver) can promote a calmer, balanced mental state 31.

Prioritizing Restful Sleep

Sleep quality plays a significant role in supporting gut health. Poor sleep can disrupt microbiota balance, but restorative sleep may promote beneficial bacteria and help the body recover from daily stressors 32. 

To encourage good sleep hygiene, I recommend that my clients:

• Reduce exposure to bright lights and screens in the evening.
• Maintain a cool, dark, and quiet sleep environment.
• Avoid stressful activities before bed, like intense exercise or difficult conversations.
• Aim for 7–9 hours of rest each night.
• Address any sleep disorders, like sleep apnea, that may interfere with quality sleep.

Step 4: Consider Antimicrobials

When I have clients whose symptoms and gut dysbiosis are still not under control after implementing a gut-friendly diet, probiotics, and lifestyle changes, we often try antimicrobials.

For stubborn overgrowths like SIBO, the most common antimicrobial recommended is a prescription antibiotic called rifaximin. 

A meta-analysis showed that rifaximin taken with probiotics resolved SIBO in 86% of patients. As I mentioned above, taking probiotics by themselves killed SIBO in more than half (53%) 8. 

Unfortunately, rifaximin is expensive, and some people don’t have the insurance coverage for it. If that’s an issue, or if clients simply want to avoid antibiotics for their potential side effects, herbal antimicrobials can be an excellent option. 

Herbal and food-based antimicrobials are gentler on the body, but they can still help reduce overgrowths of less beneficial microbes in the gut. They also do not appear to contribute to bacterial resistance in the same way as prescription antibiotics do 33.

At the clinic, we typically use a range of herbal antimicrobials in a rotation that appears to be effective 34. For example, garlic, ginger, turmeric, and green tea all have natural antimicrobial properties that can help reduce bad bacteria without disturbing beneficial microbes.

However, if I were to pick just one antimicrobial herb to start with, it would be oregano oil. This essential oil is in most herbal antimicrobials that are effective against SIBO 35, and it can even kill fungal overgrowths in lab experiments 36. 

In the clinic, we’ve also found that oregano oil can successfully counter dysbiosis, Candida overgrowths, and gut symptoms in many of our clients.

Oregano oil is in two products we offer to our clients:

• Biota-Clear 1a (100% oregano oil)
• Biota-Clear 2b (oregano oil combined with caprylic acid, black walnut, pau d’arco, and biotin for a broader antimicrobial effect)

The primary distinction between herbal antimicrobials and prescription antibiotics like rifaximin lies in their timeframe for effectiveness. Rifaximin typically gives results within 10–14 days, whereas herbal antimicrobials often take longer. Typically, we expect clients to use herbal antimicrobials for at least a month before seeing clear benefits. 

Change the Gut Environment to Get Rid of Bad Bacteria

A healthy gut environment supports beneficial microbes and helps keep overgrowths in check. By focusing on diet, probiotics, and stress reduction—and antimicrobials when needed—many people can restore gut balance. 

To explore these strategies further, check out Healthy Gut, Healthy You, my science-backed guide to restoring balance naturally. Want personalized support? Book a visit with our clinic team and get expert guidance tailored to your gut.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.