Please ensure Javascript is enabled for purposes of website accessibility


He stands against a blurred, green outdoor background
Published By: Dr. Jeffrey Mark
Date: June 03, 2024

Maintaining a healthy gut is essential for overall well-being as it plays a crucial role in digestion, immunity, and even mental health. Bad bacteria in the gut can lead to various health issues, including digestive discomfort, weakened immune response, and more. Fortunately, there are natural ways to combat these harmful bacteria and promote a balanced gut microbiome. This article explores various methods such as probiotics, antimicrobial herbs, dietary changes, and lifestyle factors that can help naturally kill bad bacteria in the gut.

Key Takeaways

  • Probiotics can help balance gut bacteria by stimulating the body's natural processes to restore gut function.
  • Antimicrobial herbs like garlic, oregano oil, and berberine can kill harmful bacteria but may also affect good bacteria.
  • Dietary changes, including the consumption of fiber-rich and fermented foods, can promote a healthy gut environment.
  • Lifestyle factors such as regular exercise, sufficient sleep, and stress management are crucial for maintaining gut health.
  • Natural antimicrobials have benefits but should be used cautiously to avoid disrupting the balance of the gut microbiome.

The Role of Probiotics in Balancing Gut Bacteria


How Probiotics Work

Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. They work by improving the integrity of the gut lining, reducing intestinal permeability, and reducing inflammation. These aspects are central to a balanced ecosystem in the gut, which is essential for combatting gut dysbiosis. When supported, the environment is healthier, which is less hospitable to bad bacteria.

Common Probiotic Strains

Considering appropriate strains of probiotic bacteria for specific symptoms or imbalances is an important aspect of the selection process. For example, the strain L. acidophilus NCFM has been found to have several benefits, including:

  • Reducing inflammation
  • Improving gut lining integrity
  • Producing antimicrobial compounds

In general, lactobacillus species tend not to colonize the colon for an extended period of time, so they need to be ingested or better yet, supported with prebiotics or food they prefer. Like in the movie where a baseball field is built and the ghosts of the great ball players come to it. “If you build it, they’ll come.” 

Benefits of Probiotics

The increase in these beneficial organisms can improve the overall balance of the gut ecosystem and reduce bad or less beneficial bacteria. This is in part due to these organisms producing antimicrobial compounds that limit the presence of less beneficial bacteria in the gut microbiome. Therefore, working to support the balance of the gut bacteria, including lowering the levels of bad bacteria, can play a central role in a wide range of digestive and non-digestive conditions.

The real gut doctor offers personalized holistic health solutions focusing on gut health, hormonal balance, and cardiometabolic issues. Schedule a discovery call to start your journey to vibrant health.

Antimicrobial Herbs and Their Effects


Antimicrobial herbs have been used for centuries to combat harmful bacteria in the gut. These natural remedies can be effective in changing the gut environment to get rid of bad bacteria. However, it's important to use them correctly to avoid potential negative impacts on the gut microbiome.

Garlic and Its Antimicrobial Properties

Garlic is well-known for its antimicrobial properties. It contains compounds like allicin, which can target and eliminate harmful bacteria. Incorporating garlic into our diet can help maintain a balanced gut microbiome.

The Power of Oregano Oil

Oregano oil is another potent antimicrobial herb. It contains carvacrol and thymol, which are effective against a variety of pathogens. Using oregano oil can help address specific gut microbes and general imbalances, including gut dysbiosis.

Using Berberine for Gut Health

Berberine, found in plants like goldenseal and barberry, has strong antimicrobial effects. It can be used to target specific gut bacteria and support overall gut health. However, long-term use should be monitored to prevent depletion of beneficial gut bacteria.

While certain herbs can be used to target specific gut microbes, many approaches use a combination of herbs to take several microbes or general imbalances into consideration.

Dietary Changes to Support a Healthy Gut


Foods That Promote Good Bacteria

A healthy diet and lifestyle encourage a healthy gut microbiome. For example, reducing the amount of processed, sugary, and high-fat foods that we eat may lead to better gut health by helping to starve bad gut bacteria. Eating a diet high in fiber likely contributes to a healthy gut microbiome as well. You may also positively impact your gut by eating foods high in micronutrients called polyphenols present in:

  • Vegetables
  • Fruits
  • Coffee
  • Tea
  • Wine

The Impact of Fiber on Gut Health

Eating a diet high in fiber is crucial for maintaining a healthy gut. Fiber acts as a prebiotic, feeding the beneficial bacteria in our gut. This results in specific changes to the gut microbiome, including:

  • Improved microbiome diversity
  • Increased levels of beneficial bacteria (e.g., Bacteroidetes, lactobacilli, Bifidobacteria, faecelibacterium)
  • Reduced levels of less beneficial bacteria (e.g., firmicutes, proteobacteria)
  • Improved gut balance
  • Reduced levels of opportunistic bacteria
  • Improved strength of the gut lining (reduced leaky gut)

Fermented Foods and Their Benefits

Fermented foods are another excellent way to support gut health. These foods contain live bacteria that can help balance the gut microbiome. Some popular fermented foods include:

  • Yogurt
  • Kefir
  • Sauerkraut
  • Kimchi
  • Miso

It's also a good idea to support healthy biodiversity in your gut through your diet and lifestyle choices. Importantly, minimizing the damage to the beneficial bacteria residing in your large intestine when making dietary, medical, or lifestyle changes is key for long-term success.

Lifestyle Factors Influencing Gut Health


The Importance of Regular Exercise

Regular exercise is a cornerstone of maintaining a healthy gut. Physical activity helps to increase the diversity of gut bacteria, which is crucial for overall gut health. This diversity within the human gut microbiota plays a significant role in digestive health. Exercise can also reduce inflammation and improve the gut barrier function, preventing harmful bacteria from entering the bloodstream.

How Sleep Affects Gut Bacteria

Quality sleep is essential for a balanced gut microbiome. Poor sleep can disrupt the circadian rhythm, which in turn affects the gut bacteria. Ensuring we get enough sleep helps to maintain the balance of good and bad bacteria in the gut.

Stress Management for a Healthy Gut

Chronic stress can negatively impact gut health by altering the gut microbiome. Effective stress management techniques, such as mindfulness and meditation, can help maintain a healthy gut environment. It's important to recognize that lifestyle and dietary changes may positively affect not only your gut health but your overall health.

Supporting a healthy gut environment goes back to a few different elements: diet and nutrition, lifestyle, including exercise and sleep, and probiotics.

Intermittent fasting or Time Restricted Eating

What you eat seems fairly obvious for influencing the microbiome but when you eat and allowing for a period of fasting also helps with a healthier  gut microbiome.  Akkermansia species increase with fasting as other bacteria can be starved out and diminished in the absence of food. Allowing a few hours without food in between meals helps Akkermanisia species which help you by strengthening the integrity of the intestinal barrier, modulating  insulin resistance and protecting from metabolic inflammation.

Natural Antimicrobials: Benefits and Risks


Understanding Natural Antimicrobials

Natural antimicrobials are substances derived from natural sources that can kill or inhibit the growth of harmful bacteria. These include certain herbs, essential oils, and plant extracts. They are often used as an alternative to prescription antibiotics, which can have adverse effects on our gut health.

Potential Risks of Overuse

While natural antimicrobials can be effective, overuse can lead to several issues. These include:

  • Disruption of gut microbial diversity
  • Development of bacterial resistance
  • Potential allergic reactions

It's crucial to use these substances judiciously and preferably under the guidance of a healthcare professional.

Balancing Antimicrobial Use with Gut Health

To maintain a healthy gut while using antimicrobials, we should consider the following steps:

  1. Consult a healthcare provider to determine the appropriate antimicrobial for your needs.
  2. Incorporate probiotics and prebiotics into your diet to support gut health.
  3. Monitor your body's response and adjust usage as necessary.

Preparing your gut with lifestyle changes and probiotics can help reduce or prevent these side effects, and in some cases, can be enough to eliminate the need to use a drug or herb like this in the first place.

By balancing the use of natural antimicrobials with other gut-friendly practices, we can support our overall health and well-being, including our gut microbiota.

The Science Behind Gut Microbiome Diversity


Why Diversity Matters

The science on the gut microbiome has taken massive strides forward since the turn of the century. One of the most important discoveries we've made is that bacterial diversity is key to a healthy gut. If you want a robust microbiome with a good chance of protecting you from disease, you need as many different species and strains of microbes down there as possible. Research suggests that when it comes to gut health, we should aim to have as many different species of bacteria as possible. Trying to get rid of bad bacteria usually affects the good ones too and reduces diversity. Reduced diversity can result in dysbiosis: an imbalance in the communities of bacteria and microbes that make up your microbiome. Dysbiosis is associated with many conditions both inside and outside the gut.

Factors That Influence Microbiome Diversity

In a healthy gut microbiome, different types of microorganisms support each other. Consider how different plants in a garden cross-pollinate or nourish the soil for each other. Similarly, various types of bacteria in your gut interact to maintain a balanced ecosystem. For example, some types feed other types by breaking down compounds, or their byproducts change the acidity of the “soil.”

Maintaining a Diverse Microbiome

The question of what exactly constitutes a healthy gut microbiome remains unanswered. We know that hosting a diverse set of bacteria in your digestive tract is associated with better health outcomes, and we know that a lack of biodiversity is associated with a number of diseases and dysfunctions. But the scientific and medical communities have yet to identify a particular set of (or number of) microbes that is definitively the “ideal” for any individual. The “ideal” seems to be as unique as the individual.

Signs of Imbalanced Gut Bacteria

imbalance gut bacteria

Common Symptoms of Dysbiosis

When our gut bacteria are out of balance, we may experience a range of symptoms. These can include an upset stomach, unintentional weight changes, and fatigue. Stomach disturbances such as gas, bloating, constipation, diarrhea, and heartburn are also common indicators. A balanced gut will have less difficulty processing food and eliminating waste, likely leading to fewer symptoms.

How to Diagnose Gut Imbalance

Diagnosing gut imbalance often involves a combination of symptom assessment and medical testing. Common tests include stool analysis, breath tests, and blood tests to check for inflammation and other markers. Consulting with a healthcare provider is crucial for an accurate diagnosis.

Steps to Restore Gut Health

  1. Dietary Changes: Incorporate more fiber-rich foods and reduce sugar intake.
  2. Probiotics: Consider taking probiotic supplements or eating fermented foods.
  3. Hydration: Drink plenty of water to aid digestion.
  4. Exercise: Regular physical activity can help maintain a healthy gut.
  5. Stress Management: Practice stress-reducing techniques like meditation or yoga.

A healthy gut contributes to a strong immune system, heart health, brain health, improved mood, healthy sleep, effective digestion, and potential prevention of some cancers and autoimmune diseases.


In conclusion, maintaining a balanced and diverse gut microbiome is essential for overall health. While there are various methods to eliminate bad bacteria in the gut, such as using pharmaceutical antibiotics or antimicrobial herbs, these approaches can also harm beneficial bacteria. A more holistic approach, including a healthy diet, regular exercise, and adequate sleep, is recommended to create an environment that supports good bacteria and inhibits the growth of harmful ones. Probiotic supplements can also play a crucial role in restoring gut balance by stimulating beneficial processes in the body. Ultimately, fostering a diverse microbiome is key to long-term gut health, as a well-balanced human gut microbiota contributes significantly to overall digestive health.


Frequently Asked Questions

How can I get rid of bad bacteria in the gut naturally?

The best way to get rid of bad bacteria in the gut naturally is by creating an environment that supports a balanced and diverse microbiome. This can be achieved through dietary changes, regular exercise, proper sleep, and stress management. Using antimicrobial herbs and supplements can help, but it is important to use them cautiously as they can also affect good bacteria.

What are some common symptoms of imbalanced gut bacteria?

Common symptoms of imbalanced gut bacteria, also known as dysbiosis, include bloating, gas, diarrhea, constipation, fatigue, and food intolerances. Skin issues, mood swings, and a weakened immune system can also be indicators.

How do probiotics help in balancing gut bacteria?

Probiotics help balance gut bacteria by stimulating certain processes or responses from the body to restore gut function. They do not add more bacteria to the gut but rather promote a healthy environment for good bacteria to thrive.

What foods promote good bacteria in the gut?

Foods that promote good bacteria in the gut include high-fiber foods like fruits, vegetables, legumes, and whole grains. Fermented foods such as yogurt, kefir, sauerkraut, and kimchi are also beneficial as they contain live probiotics.

Are there risks associated with using natural antimicrobials for gut health?

Yes, there are potential risks associated with using natural antimicrobials. While they can help eliminate bad bacteria, they can also affect good bacteria in the gut. Overuse can lead to an imbalance in the gut microbiome, known as gut dysbiosis, so it is important to use them judiciously and under the guidance of a healthcare professional.

How long does it take to restore gut health after an imbalance?

The time it takes to restore gut health after an imbalance varies depending on the severity of the dysbiosis and the steps taken to address it. Generally, with consistent dietary changes, use of probiotics, and lifestyle modifications, improvements can be seen within a few weeks to a few months.

He stands against a blurred, green outdoor background
Dr. Jeffrey Mark
With over thirty years of experience, Dr. Mark is a leading expert in holistic gut health. His integrative approach combines conventional medicine, functional and regenerative medicine, and advanced therapies to heal the gut and transform patient health. Holding 5 board certifications, Dr. Mark offers the comprehensive expertise of five medical specialists during each patient visit. He is dedicated to optimizing wellbeing by addressing the gut-related root causes of chronic health issues.
Our patient coordinator is ready to help answer your questions
About The Real Gut Doctor: Dr. Jeffrey Mark and use integrative,
An image of a smiling person in a professional settingDr. Jeffrey Mark's team uses Integrative
linkedin facebook pinterest youtube rss twitter instagram facebook-blank rss-blank linkedin-blank pinterest youtube twitter instagram