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

Written by Dr. Michael Ruscio, DC on November 25, 2024

Written by Dr. Michael Ruscio, DC on November 25, 2024 — Reviewed by Heidi Turner

• Microbiome Imbalance|
• Symptoms of Microbiome Imbalance|
• How to Get Rid of Bad Bacteria|
• Step 1|
• Step 2|
• Step 3|
• Step 4|

Getting rid of harmful bacteria in the gut is a crucial step toward achieving digestive health and better overall wellbeing.

Many “bad” bacteria are relatively harmless—or even helpful—when kept in check. So a healthy gut isn’t simply about “good” or “bad” bacteria; it’s about achieving balance among different types. 

The gut microbiome is made up of various bacteria, fungi, and parasites. If it’s not diverse or strong enough, harmful microbes can overgrow and kill off beneficial ones.

This can trigger problems throughout the body, including infections, gastrointestinal symptoms, 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?

Various factors can harm the microbiome, causing microbial imbalances (dysbiosis), bacterial overgrowths, and inflammation. Possible contributors include:

• Overuse of antibiotics 1
• Chronic conditions such as irritable bowel syndrome (IBS) 2, fatty liver disease 3, or depression 4
• High stress levels that activate the fight-or-flight response 5
• Obesity 6

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 prescription 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.

Symptoms of Imbalanced Microbiota

In the clinic, our clients often report symptoms that point to imbalances in the microbiota, or the individual organisms that make up the microbiome. These symptoms include:

• IBS-type symptoms, such as bloating, gas, and belly pain
• Constipation or diarrhea (or both taking turns)
• 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 

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 people stay the course.

Step 1: Take Probiotic Supplements

Taking probiotics is one of the most effective ways to restore a healthier gut microbiome.

Probiotics can increase bacterial diversity. This helps 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 are also very effective at getting rid of 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 constipated people poop more often and have softer poop 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. 

In fact, probiotics may have less of an impact on a healthier microbiome 13. 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, 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 or cerevisiae (beneficial yeasts), and a soil-based probiotic together for optimal results.

Here’s how we outline our triple-therapy probiotic protocol:

Step 2: Eat a Microbiome-Friendly Diet

Probiotics have significant benefits, but their scope is limited without the support of a healthy diet.

There’s no “one size fits all” when it comes to finding a gut-supportive diet that will reduce levels of unhealthy bacteria and optimize the microbiome 14. But there are four key things that a gut-friendly diet should do:

• Help reduce inflammation
• Manage blood sugar levels
• Minimize food sensitivities and intolerances
• Provide healthy carbohydrates and prebiotic fibers (food for helpful gut bacteria) 

In general, a diet with a wide variety of plant types is linked to greater gut microbiota diversity and fewer harmful bacteria 15. However, too much plant fiber, especially insoluble fiber (like wheat bran) can cause problems for some people with gastrointestinal issues. This means fiber intake should be adjusted according to each person’s tolerance 16.

Similarly, people respond uniquely to dietary carbohydrates and have differing degrees of food sensitivity depending on their baseline gut health. These considerations can guide us in choosing the best diet for our unique circumstances.

At the clinic, we recommend three main diets for rebuilding gut health. The best choice depends largely on each client’s specific symptoms and baseline gut health. 

The Mediterranean Diet

This diet emphasizes a wide variety of high-fiber, microbiota-friendly foods, including colorful fruits and vegetables (rich in health-promoting polyphenols), legumes, and whole grains. It also includes oily fish, other unprocessed protein sources, and moderate amounts of dairy. 

For those without fiber-related gut issues or a dairy or wheat intolerance, the Mediterranean diet is an excellent option for gut health.

Research shows that it is both anti-inflammatory 17 and beneficial for microbiota diversity 18.

The Paleo Diet

Another whole-foods approach, the Paleo diet generally involves low to moderate carbohydrate intake and excludes or minimizes grains and dairy. It emphasizes pasture-raised meats, fish, fruits, vegetables, nuts, and seeds. 

Although the Paleo diet doesn’t have as much research supporting its microbiota-boosting qualities as the Mediterranean diet, many of our clients find it helpful for alleviating gut symptoms and improving energy. 

Its benefits likely stem from eliminating common allergens (such as dairy and gluten) and helping to stabilize blood sugar. It is also anti-inflammatory 17, which can support microbiome health.

The Low FODMAP Diet

For clients whose symptoms don’t ease up after following a Mediterranean or Paleo diet, we often suggest a trial of the low FODMAP diet. 

This diet restricts certain gas-producing carbohydrates, which cause symptoms in some individuals. A low FODMAP diet excludes foods like broccoli, cabbage, onions, garlic, cashews, beans, apples, pears, and wheat. However, it includes a variety of other plant-based foods, as well as meats, some grains, and certain dairy products that people generally tolerate well.

A wealth of evidence supports a low FODMAP diet for alleviating IBS symptoms, such as gas, diarrhea, and bloating 19. It’s also effective for managing SIBO symptoms, particularly when people take probiotics at the same time 20. 

Although a low FODMAP diet may reduce numbers of healthy Bifidobacteria in the gut at first 21, its ability to relieve symptoms makes it a great choice for many. Over time, reintroducing FODMAPs as tolerated—with guidance from a doctor or dietitian—should promote microbiota diversity and microbiome health.

Any of the above diets can also be combined with intermittent fasting to turn around an unhealthy gut faster. Intermittent fasting involves regularly switching between eating and fasting, which can support gut microbiome balance, aid weight loss, and improve metabolic health (to avoid conditions like heart disease and diabetes) 22.

An easy way to implement intermittent fasting is to delay breakfast and have an earlier dinner. One option is to fit all meals into an 8–10 hour daily window, so the digestive system can rest for 14 hours minimum overnight.

Step 3: Dial Down Stress To Balance the Microbiota

Managing stress is an essential part of supporting the gut microbiota. When we’re stressed, our fight-or-flight hormones can disrupt the way our gut bacteria function 5.

Managing stress by regularly exercising, connecting with nature and sleeping well, can all positively influence gut health.

Exercise

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

• Promoting a more diverse microbiota 23
• Encouraging healthy bacteria to produce short-chain fatty acids (SCFAs), which reduce inflammation and support immune function 24
• Supporting proteins called toll-like receptors (TLRs) that prevent the immune system from incorrectly labeling helpful gut bacteria as harmful 25
• Helping the muscles release more myokines (proteins or shorter chains of amino acids with anti-inflammatory effects) 26

Doing moderate-to-high-intensity exercise (like cardio or strength training) for 30–90 minutes three times per week can positively impact the microbiome 23.

But listening to the 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 5. 

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 27 28. 

Walking in nature may be even better. Studies show that walking in nature combines the benefits of physical activity and natural stress reduction, further enhancing gut health and overall health 29. 

But if we’re too busy to get outside, even looking at pictures of green scenery—for example on a screen saver—can promote a more calm and positive mental state 30.

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 31. 

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 got rid of SIBO in a whopping 86% of patients. Impressively, 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. 

Herbals are gentler on the body but still effective at getting rid of bad bacteria in the gut. They also do not appear to contribute to bacterial resistance in the same way as prescription antibiotics do 32.

At the clinic, we typically use a range of herbal antimicrobials in a rotation that appears to be effective 33.

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 34, and it can even kill fungal overgrowths in lab experiments 35. 

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’ve formulated for 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 require a little more patience. 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

The key to a healthy gut microbiome is making sure the gut is a welcoming, nutritious environment for good bacteria to thrive, and a place where bad bacteria can’t. Supporting a healthy gut can both get rid of bothersome microbes and prevent them from coming back. 

Diet, probiotics, and stress-busting habits are the main answers to the tough question of how to get rid of bad bacteria in the gut. 

Antimicrobials or antibiotics can then be used to clear out any remaining harmful microorganisms and restore a healthy gut microbiome.

For more information on gut health, diet, probiotics, and more, check out my book Healthy Gut, Healthy You. Or for more personal support, get in touch with us for an appointment.

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.