How to Starve Bad Gut Bacteria by Preparing Your Gut

How to Starve Bad Gut Bacteria by Preparing Your Gut the Right Way

And Why Killing Off the Bad Isn’t Enough to Sustain a Healthy Gut Microbiome

Key Takeaways

  • Improving your overall gut health is step one.
  • This means preparing your gut with diet and lifestyle changes.
  • Probiotics might be the only supplement you need.
  • If you need antibiotics or antimicrobials, use them after and with probiotics.

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.

That said, if you know or suspect you’re experiencing gut dysbiosis (an imbalance between “good” and “bad” gut bacteria) or an overgrowth of bacteria in your intestines, such as SIBO (small intestinal bacterial overgrowth), then starving out the bad bacteria (and/or excess bacteria in general) is an important step in treating your overall condition.

It’s also a good idea to support healthy biodiversity in your gut through your diet and lifestyle choices, which we’ll get into in this article. 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.

We’ll map out the process of how to starve bad gut bacteria, which includes a foundational approach to improving gut health and your gut ecosystem. This includes dietary changes, sleep and exercise improvements, probiotic supplements, and in some cases, antimicrobial/antibiotic therapy.

How to Starve Bad Gut Bacteria: Preparing Your Gut

The best way to get rid of bad bacteria is to follow a stepwise, foundations-up approach to making your digestive system more hospitable to good bacteria and less hospitable to bad bacteria in the long-term. In other words, killing off the bad bacteria with a prescription or herbal antibiotic may help in the short-term, but for long-term gut balance, a more holistic approach is needed.

This isn’t to say that an antibiotic of some sort won’t be necessary or helpful. Research shows that a strong immune system bolstered by probiotics (especially Lactobacillus strains and Saccharomyces boulardii) can improve the efficacy of antibiotics and reduce the potential negative side effects of taking them [1 Trusted SourcePubMedGo to source, 2 Trusted SourcePubMedGo to source, 3 Trusted SourcePubMedGo to source].

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While it may seem like eating whole foods, exercising regularly, and improving sleep quality is generic, tired advice, there’s a reason these three lifestyle changes are so often recommended, and it’s not all about weight loss either. 

In the case of gut microbial balance, these key lifestyle changes are associated with greater biodiversity and improved gut health. In short, they go a long way toward correcting dysbiosis, even without a pharmaceutical intervention. 

Your gut microbiome may be composed of hundreds of species that are distinct and separate from you as a homo sapien, but these little bugs are attuned to your daily life and behaviors as if they were part of you. You affect them, and they affect you. This type of relationship is called a commensal relationship, so a balanced lifestyle can beget a balance of bacteria in your gut.

Eat an Anti-inflammatory Diet

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As an example of how your diet affects your gut microbes, let’s talk about inflammation. Certain foods prevalent in the Western diet, like sugar, alcohol, and highly processed meats and carbs lead to inflammation in your body — they’re pro-inflammatory foods. 

These foods feed bacteria in your gut that create more inflammation and wreak havoc — think bloating, gas, constipation or other irritable bowel syndrome (IBS) symptoms, along with damaged epithelial tissue that can lead to leaky gut. When you feed inflammatory bacteria, they grow and reproduce, creating more inflammation, more damage, and the cycle continues. 

So it follows that anti-inflammatory foods and drinks, such as those you’d find in the Paleo diet, the Mediterranean diet, or even a mindful vegetarian diet, would lead to improvements in the overall health of your intestinal microbiota. A low-FODMAP diet is generally the best option for those with SIBO or bacterial overgrowth. 

FODMAP foods contain certain fibers: fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These fibers are short-chain carbohydrates (sugars) that the small intestine absorbs poorly. They also feed certain bacteria, which, if they’re living in the wrong part of your intestinal tract (i.e. the small intestine rather than the large intestine, as is the case in SIBO), can create digestive discomfort like bloating, diarrhea, and constipation. 

Avoiding FODMAPs or dramatically reducing them will starve out the bad gut bacteria over time, but this diet isn’t meant to be used forever. It’s meant as a temporary strategy to help solve gut dysbiosis as part of a larger approach. Many FODMAP foods feed the good bacteria living in your colon and are generally considered healthy foods to consume (such as brassicas, onion, and garlic, to name a few). 

It’s also a good idea to eat foods rich in live bacteria. Fermented foods such as raw sauerkraut, kimchi, or kombucha can supplement good gut bacteria, in addition to probiotic supplementation to add more concentrated amounts (in the billions or trillions) of beneficial microorganisms into the human gut.

When paired with the lifestyle shifts we’re about to discuss — probiotics, and possibly antibiotics or antimicrobials — a low-FODMAP diet is the best approach for how to starve bad gut bacteria.

Research on the Mediterranean diet shows that this diet — rich in fresh veggies and fruit, olive oil, whole grains, legumes, fresh meat, and fish — is associated with an enriched microbiota that promoted “an anti-inflammatory environment low in taxa with pro-inflammatory properties capable of altering intestinal barrier functions” [4 Trusted SourcePubMedGo to source].

Another study comparing the gut bacteria of vegans and omnivores found that while there were differences between the two, there wasn’t enough information to determine if one diet is better than the other in terms of how they create healthier and more productive gut microbiotas. More randomized controlled studies are needed to better assess the gut flora that results from different diets, but again, there are notable associations between those with diets rich in pro-inflammatory foods vs. anti-inflammatory foods [5 Trusted SourcePubMedGo to source].

Exercise and Sleep to Support Your Gut

Exercise and sleep are both positive inputs on digestive health. A systematic review of eight observational studies looking at the effects on exercise and gut biodiversity found higher variability and prevalence of Firmicutes (genera Ruminococcaceae or Fecalibacteria) in active people compared to sedentary people, and especially in athletes. This was considered a healthy shift in microbes [6 Trusted SourcePubMedGo to source].

In another systematic review that evaluated nine observational studies and nine clinical trials, researchers found that increased physical activity or fitness were positively correlated with higher bacterial alpha diversity (total number of microbes), and with a greater abundance of some phyla and certain short-chain fatty acids (which feed certain beneficial bacteria, including the ones listed above) in stools [7 Trusted SourcePubMedGo to source].

The link between better sleep and microbial diversity in the gut is a little bit harder to support with peer-reviewed research because, as we mentioned at the very top, what constitutes “healthy” is not standardized or agreed-upon when it comes to the gut microbiome.

That being said, we know that good quality sleep supports your immune system. We know that sleeping well supports mental health and wellness. We know that a good night’s sleep aids in decision-making, in the body’s ability to turn over cells, heal, regenerate, and rejuvenate, and all of those things can support you in making better choices around food and exercise. Our clinical work has seen improvements in sleep and stress management as key factors in supporting gut health, and we consistently recommend strategies for improvements in these areas.


Probiotics are among the first lines of defense for maintaining or improving gut health. Along with the lifestyle and diet changes we’ve already mentioned (including foods rich in live bacteria), probiotic supplements should be part of your regimen for starving out bad gut bacteria. 

In the next section, we’ll go over the time and place for antibiotics and antimicrobials and the potential side effects those interventions may have. 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 [8 Trusted SourcePubMedGo to source, 9 Trusted SourcePubMedGo to source, 10 Trusted SourcePubMedGo to source].

Furthermore, if antibacterial measures are needed, there’s evidence to suggest that probiotics actually increase their effectiveness. A systematic review of 140 studies showed that probiotics enhanced the effects of an antibiotic used on H. pylori-infected patients [1 Trusted SourcePubMedGo to source]. Another review of 40 studies showed that the use of probiotics prior to and throughout the eradication regimen, as well as probiotics used for more than two weeks, yielded stronger eradication effects. The most effective probiotics were Lactobacillus and multiple strains, and the greatest eradication effect was observed in China [2 Trusted SourcePubMedGo to source].

We recommend a triple-therapy approach to supplementing probiotics, covering the three main categories of microbes that are living in your gut. Category one includes the long list of species in the genera Lactobacillus and Bifidobacterium. Category 2 is a fungal probiotic called Sacchromyces boullardi, and Category 3 is soil-based probiotics. In our clinical work, we’ve observed that this approach seems to be more conducive to balance and healing in the microbiota and the gut than a single category alone.

Antibiotics and Antimicrobials

Herbal and/or pharmaceutical antimicrobials/antibiotics can help to get rid of bad bacteria, but are more effective when your foundations are in place. The foundations we’ve already covered are diet, exercise, probiotics, and sleep. Importantly, these key steps should all be in place as the foundation before you introduce antibiotics or antimicrobials. 

These types of medications and/or herbs are designed to kill off pathogens or other harmful microbes, but they can sometimes do some damage in the process. Namely, prescription antibiotics come with potential side effects, such as increased risk for all-cause and heart-related death later in life, allergic reactions, nausea, vomiting, abdominal pain, rash, bacterial resistance, and reduced gut microbial diversity, especially in middle and later adulthood, which may impair immunity, and even have adverse psychiatric effects [11 Trusted SourcePubMedGo to source, 12 Trusted SourcePubMedGo to source, 13 Trusted SourcePubMedGo to source, 14 Trusted SourcePubMedGo to source].

This isn’t to say that these drugs and herbs don’t have their place in medicine or gut health, but it is to say that they’re most effective when used after all other interventions have been put in place, and after you’ve prepared your gut for them.

Maintaining Gut Health

The goal in learning how to starve bad gut bacteria is a long-term balance of bacteria. A healthy gut microbiome means a healthy gut lining, which means less inflammation and fewer health issues associated with a leaky gut or other forms of gut dysbiosis. These are all good things to support your overall health and wellbeing.

While you can’t micromanage an ecosystem, you can create an environment that’s encouraging of what you want (healthy bacteria) and discouraging of what you don’t want (unhealthy bacteria) through diet, lifestyle, and probiotic supplements. Preparing your gut to handle antimicrobials is key, but maintaining these changes to support a healthy ecosystem in your gut long-term is the best strategy for how to starve bad gut bacteria.

If you need some guidance figuring out where to start, we’re here to help. Learn more about how to become a patient with us, and let’s get started.

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➕ References
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