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How to Get Rid of Bad Bacteria in the Gut for Good

Written by Dr. Michael Ruscio, DC on January 17, 2022

Written by Dr. Michael Ruscio, DC on January 17, 2022 — Reviewed by Heidi Turner

Support a Healthy Gut Environment With Diet, Exercise, Sleep, and Probiotics First

• Root Causes of Dysbiosis|
• Terrain Theory|
• Probiotics|
• Build a Foundation of Health|
• Change the Gut Environment|

It’s easy to fall down an internet rabbit hole when searching for an answer on how to get rid of bad bacteria in the gut. Many strategies, from fasting to antibiotics, claim to eliminate dysbiosis, a state of imbalance in the microbiome. 

But most of the time, patients take one step forward only to take two steps back when they try to kill off bad bacteria in the gut — without addressing the foundations of health first. These foundations include things like diet, sleep, and exercise. Once those are in place, therapies like probiotics and antimicrobial agents (when necessary) are usually much more effective. 

The key point is — we have to create an environment in the body that encourages healthy bacteria in the gut and discourages unhealthy bacteria. Sometimes, just improving your diet and lifestyle alone will change the gut environment enough to balance the microbiome. 

In this article, we’ll discuss the causes behind overgrowths of bad gut bacteria, building a better gut environment to address dysbiosis, and how to get rid of bad bacteria in the gut by first securing the foundations of health and then using antimicrobials and other therapeutics as needed. 

Address the Root Causes of Dysbiosis First

Let’s first take a look at the causes behind bad bacteria in the large intestine, specifically as they pertain to chronic illness. 

There has been some question in the medical world for a while around whether bad gut bacteria leads to disease, or vice versa. From the scientific research currently available, it seems that the disease state comes first, then the microbiome begins to tip towards imbalance.

In general, studies have shown that there is less overall diversity in the microbiota of chronically ill people, and sometimes there are imbalances in certain species of bacteria, such as an overgrowth of E. coli bacteria 1 2 3 4.

However, we haven’t yet found a causal link between certain microbial environments and different illnesses, such as type 2 diabetes, irritable bowel syndrome (IBS), or Crohn’s disease. We can only say that the two are associated, and it may actually be more likely that the disease state — inflammation, inadequate nutrients, tissue damage, an overactive immune system, etc. — leads to dysbiosis and potentially an overgrowth of bad bacteria 5.

This means that addressing the root causes of illness and supporting the whole person with good nutrition, rest, movement, and social connection will likely go a long way toward correcting dysbiosis.

Terrain Theory: Building a Better Environment for Gut Bacteria

It’s tempting to place blame on one offending microbe, like candida or a parasite, and simply eliminate that microbe to regain a healthy gut. Attack the invader directly, kill it, and everything should go back to normal, right? 

In reality, this approach can create more problems than it solves. When we go straight to antibiotics, whether pharmaceutical or herbal, they often create a situation where only some of the bad bacteria dies off, and it resurges with a vengeance after the antibiotic course has been completed. 

Or, even if the antibiotic works and completely gets rid of the microbe, odds are good that another microbe will simply take its place, and the problem starts all over again. This is often the case with candida overgrowth post-antibiotics. Patients end up playing a frustrating game of ping-pong between antibiotics and antifungal medicines. 

So what’s the alternative? Instead of pinpointing and attacking a single type of bacteria, we want to look at the overall environment in the gut, the gut terrain, if you will. By supporting an environment where good bacteria thrive and bad bacteria do not, you can often eliminate the need for targeted antimicrobials. Bad bacteria are much less likely to proliferate in a healthy gut. 

Probiotics: Fight Bad Bacteria With Good Bacteria

We have found probiotic therapy to be a crucial step for gut healing in our clinic, and probiotics have the research to back them up. 

Probiotics have been shown to be equally as effective as antibiotics in treating some kinds of dysbiosis, without the side effects of antibiotic use. A systematic review and meta-analysis including 8,924 patients found that compared with controls, people who took probiotics as part of their H. pylori treatment had higher rates of eradication and lower incidences of total side effects 6.

Probiotics also help antibiotics/antimicrobials work more effectively. A study featuring 20,215 patients with H. pylori infections found that those who took probiotics alongside antibiotics had better results than patients who only took antibiotics 7. Another study on 40 SIBO patients found that those taking a combination of S. Boulardii and metronidazole (an antibiotic) had a success rate of eradicating SIBO more than double that of those taking metronidazole alone 8.

We recommend Probiotic Triple Therapy to our patients with gut dysbiosis, SIBO, H. Pylori, and other gut infections and imbalances. By combining the three different categories of probiotics — Lacto/Bifido blends, Saccharomyces boulardii, and soil-based probiotics — we’ve seen great improvements in our patients’ gut health. 

Step-by-Step: Build a Foundation of Health for Your Gut Bacteria

Supporting a healthy gut environment goes back to a few different elements: 

• Diet and nutrition
• Lifestyle, including exercise and sleep
• Probiotics

Let’s take a look at each of these areas. 

Step 1: Diet, Exercise, and Sleep

These are a few of the main pillars in the foundation of your health. Before you do anything else, check in with yourself to see: 

• Are you eating an anti-inflammatory diet that prioritizes adequate macronutrients (protein, carbohydrates, and healthy fats) and micronutrients (vitamins and minerals)? 
• Are you incorporating movement into your daily routine like walking, yoga, or strength training? 
• Are you getting enough sleep, between seven to nine hours per night? How is your sleep quality? 

If you need to shift your diet and don’t know where to start, we start off most of our patients on a Paleo diet. This diet is great for most people because it’s anti-inflammatory and nutritious without being too restrictive. It’s amazing how many people are able to change their gut flora just by changing the food they eat every day. They’ll often experience health benefits like weight loss, improved mental health, and better energy, too.

​​The Paleo diet includes many prebiotic foods that feed the trillions of beneficial bacteria in your digestive system. This works great for some people, but for people with SIBO, for example, prebiotic foods will likely exacerbate symptoms. In this case, a low FODMAP diet may be more helpful. You can identify which diet might be best for you by examining our four principles of a healthy diet. 

Movement and exercise also have a significant impact on the digestive system and your gut microbiome. A systematic review looked at nine observational studies and nine clinical trials to understand how exercise influences the gut microbiota of healthy adults. They found that increased physical activity or fitness was positively associated with higher bacterial diversity and certain short-chain fatty acids in stools 9.

Lack of sleep is one of the lifestyle factors that contributes to chronic illness, which is associated with gut dysbiosis. It’s pretty safe to assume that making sure you get good quality sleep for seven to nine hours a night will improve your health overall, including your gut health. 

Step 2: Probiotics

Once your foundation of diet, exercise, and sleep is in place (or you’ve at least made progress on them), you can add in probiotics. 

If you’re still having symptoms of bad bacteria in the gut, like bloating, constipation, diarrhea, leaky gut, chronic fatigue, intense cravings, and even skin issues like eczema, probiotics can be a great complement to your healthy diet and lifestyle. 

If you know you aren’t sensitive to supplements, you can start right away at a full dose of a high-quality, multi-species probiotic supplement, which usually has Lactobacillus and Bifidobacterium species. Or you can try Probiotic Triple Therapy for even more variety (Lactobifido blend + S. boulardii and soil-based probiotics). 

If you know you’re sensitive to supplements, or you’re not sure how your body will react, it’s better to go slow and start at a half or even quarter dose until your digestive tract has a chance to adjust. Then increase slowly to find your therapeutic dose. 

You can also incorporate probiotic foods like kimchi, kefir, sauerkraut, and kombucha, but you would need to eat a lot of these foods to amount to the same probiotic power as a high-quality supplement. 

Step 3: Antimicrobials and Antibiotics

After you’ve completed steps 1 and 2, and you’ve given your body some time to adjust to those changes, then you might consider antimicrobials or antibiotics if you’re still having symptoms. 

Antimicrobial herbs are usually more forgiving than antibiotic drugs, and they often work just as well or better. But, they can still have a number of side effects, so it’s important to work with a practitioner and match the right antimicrobial to your body’s needs 10.

Some examples of antimicrobial herbs include oil of oregano, berberine, peppermint, and sweet wormwood (artemisia). 

Change the Gut Environment to Get Rid of Bad Bacteria

Supporting your health foundations, like diet, exercise, and sleep, is the first step toward getting rid of bad bacteria in the gut. If that doesn’t solve the problem by itself, then probiotics should be the next step to crowd out harmful bacteria and restabilize the microbiome. Finally, if that doesn’t completely solve the issue, antimicrobials or antibiotics can be used to gently clear the unwanted microorganisms from the gut. 

The key to a healthy microbiome is making sure the gut is a welcoming, nutritious environment for good bacteria to thrive, and a place where bad bacteria can’t. That way you’ll not only get rid of any bothersome microbes now, you’ll prevent them from coming back in the future, too. 

For more information on gut health, diet, probiotics, and more, check out my book Healthy Gut, Healthy You. 

The Ruscio Institute has developed a range of high-quality formulations to help our patients 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.