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A Guide To Starving Bad Gut Bacteria And Feeding The Good

The quality of bacteria that compose your gut microbiome determines almost every aspect of your physical wellness and mental health.

Controlling such a diverse community of trillions of microorganisms, including bacteria, viruses, fungi, and other microbes, can seem intimidating. But it's absolutely worth the time spent informing yourself and taking action to optimize your digestive health.

The delicate balance of these microbial communities is crucial, and any disruptions in this balance, known as dysbiosis, have been linked to a wide range of gastrointestinal health issues. Here are the steps I walk my functional medicine patients through to learn how to crowd out the bad and balance their microbiome with the good.

How Do You Know If Your Gut Microbiome Is Out Of Whack?

Common symptoms of an imbalanced gut include (but are not limited to):

  • Acid reflux

  • Anxiety

  • Autoimmune conditions (ulcerative colitis & Crohn's disease)

  • Bloating

  • Brain fog

  • Depression

  • Constipation

  • Fatigue

  • Food sensitivities

  • Gas

  • Headaches

  • Hormone imbalances

  • Joint pain

  • Nutrient deficiencies

  • Skin problems (acne, rashes, eczema)

  • Weight loss resistance & obesity

  • Other chronic diseases

Step 1: Gut Bacteria Testing

Testing your gut flora can provide valuable insights into the state of your microbiome. It helps identify imbalances between healthy bacteria and harmful gut bacteria, allowing for a more targeted approach to improve your healthcare experience.

Types of tests include:

  • Stool Tests: These tests analyze the composition of bacteria in your fecal matter, providing a detailed report on the diversity and abundance of different bacterial species.

  • Breath Tests: These tests measure the levels of gases, such as hydrogen and methane, produced by bacteria in your gut. They commonly diagnose conditions like Small Intestinal Bacterial Overgrowth (SIBO). Note: Taking probiotics may actually worsen SIBO.

Step 2: A Gut-Healing Diet

Food is medicine and your gut’s first defense. By incorporating diverse whole foods while eliminating inflammatory foods, you can heal your gut's lining and create a more inhospitable environment for harmful bacteria like E. coli. These are the most effective ways to transform your diet and heal your gut:

Eat More Fiber-Rich Foods

Think of good gut bacteria as living organisms inside you that need a high-fiber diet to grow.

Studies on dietary fiber (found in plant foods like artichokes, chia seeds, and Brussels sprouts) show that these food sources act as prebiotics to fuel the beneficial bacteria in your gut so they can multiply and thrive. (1)

Beneficial bacteria in your large intestine ferment the dietary fiber, producing short-chain fatty acids (SCFAs) as a byproduct. These SCFAs further maintain a healthy digestive system by supporting immune function and healthy inflammation levels.

For a high-fiber, whole-food gut healing diet, many of my patients have found success with low-FODMAP (which I discuss in detail below) and Mediterranean diets.

Limit Your Sugar Intake

Bad bacteria like to eat, too. Their primary food source is sugar, an overused ingredient in most Western diets. Eating too much sugar can cause the bad bacteria in the digestive tract to multiply and overtake your microbiome.

Instead of total sugar deprivation (which is unsustainable for most), I recommend switching from processed sugar to healthier alternatives like pure maple syrup or raw honey. Be cautious about zero-sugar options, as some of these can cause further digestive distress and are actually associated with weight gain and obesity.

Eliminate FODMAP Foods

FODMAP foods are a group of short-chain carbohydrates and sugar alcohols that are poorly absorbed in the small intestine, leading to fermentation and gas production by gut bacteria. Studies show a low-FODMAP diet reduces bad bacteria in the gut by minimizing the intake of fermentable carbohydrates that can feed bad bacteria. (2)

FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. Common high-FODMAP foods include:

  • Oligosaccharides: Whole grains like wheat & barley, onions, garlic, and legumes like lentils.

  • Disaccharides: Dairy products like milk, yogurt, and soft cheeses (due to lactose).

  • Monosaccharides: Certain fruits like apples, pears, and high-fructose corn syrup.

  • Polyols: Sugar alcohols in fruits like cherries and plums and artificial sweeteners like sorbitol and mannitol.

Try Fermented Foods

Probiotics are live, beneficial bacteria that can be found in certain fermented foods like sauerkraut, kefir, yogurt, tempeh, kombucha, and kimchi to give your gut a targeted boost of good bacteria. Eating these foods gets more good bacteria into your gut.

Eat More Antibacterial Foods

Several foods possess natural antibacterial properties that fight off harmful bacteria while preserving the beneficial ones. One such food is garlic, which contains a compound called allicin, known for its antimicrobial properties. (3)

Other foods with natural antibacterial and antimicrobial properties include:

  • Onions: Rich in sulfur compounds that have antibacterial effects.

  • Ginger: Known for its antibacterial and anti-inflammatory properties.

  • Turmeric: Contains curcumin, which has potent antimicrobial and anti-inflammatory effects.

  • Coconut oil: Contains medium-chain fatty acids, such as lauric acid, that have antibacterial properties.

  • Honey (particularly Manuka honey): Has natural antibacterial properties due to its hydrogen peroxide content and other compounds.

Eat Foods High In Polyphenols

Polyphenols are antioxidants that act as prebiotics to feed your good gut bacteria. Some of my favorite sources of these antioxidants include blueberries, chocolate (cocoa), grapes, and green tea.

One study found that cocoa intake increased the amount of Bifidobacteria in your gut — a beneficial strain of bacteria linked to a reduced risk of inflammatory bowel disease and improved symptoms of constipation and diarrhea. (4)

Remove Alcohol And Drink More Water

Removing alcohol from your diet can help reduce inflammation and support the growth of good bacteria.

Staying hydrated by drinking plenty of water works synergistically with dietary fiber to promote the growth of beneficial bacteria. Fiber acts as a prebiotic, feeding the good bacteria, while water helps fiber do its job effectively.

Step 3: Lifestyle Changes

The following lifestyle changes may seem obvious, but they are suggested so often for a reason — they really work!

Get Enough Sleep

Our bodies operate on a natural internal clock called the circadian rhythm, which regulates various physiological processes, including digestion, metabolism, and sleep-wake cycles.

Disrupted sleep patterns can lead to imbalances in the gut microbiota, impairing its diversity and function. A regular sleep routine allows our body to enter deep, restorative sleep phases where essential processes like gut repair and microbial balance occur optimally.

Regular Exercise

Studies have shown that physical activity increases the production of short-chain fatty acids (SCFAs) needed to maintain the integrity of the gut lining and reduce inflammation. (5) Regular exercise also promotes better digestion and regular bowel movements, helping to prevent the overgrowth of harmful bacteria.

Stop Stressing

It doesn’t matter how well you eat or sleep if you are constantly under the attack of stress. Chronic stress is deeply connected to poor gut health, causing intestinal permeability and chronic inflammation.

Focus on managing your stress levels by incorporating a daily mindfulness practice like meditation or breathwork and practice a JOMO (Joy of Missing Out) lifestyle that promotes self-care and healthy boundaries!

Don’t Over Sanitize

Getting your hands in the dirt exposes you to diverse beneficial microbes, which can help strengthen your immune system and promote a healthy balance of gut bacteria.

While good hygiene practices are important for preventing the spread of harmful bacteria and viruses, excessive use of antibacterial soaps, sanitizers, and disinfectants can disrupt the delicate balance of your gut microbiota. Sanitizing products may kill harmful pathogens but also wipe out beneficial bacteria.

So get your hands in the dirt, and skip the sanitizers when you do!

Quit Smoking

Smoking has numerous negative effects on your health, including your gut health. Quitting smoking can significantly improve your gut microbiome and overall health.

Step 4: Supplements

In cases of severe gut dysfunction, like nutrient deficiencies or bacterial dysbiosis, supplements can be a great tool in helping you overcome these problems quicker than food alone.

Quality probiotics, in particular, can help introduce beneficial bacteria to your gut.

One study showed that probiotics (Lactobacillus being the optimal strain) can speed the eradication of the harmful bacteria Helicobacter pylori (a type of bacteria that infects the stomach lining and can cause ulcers and stomach inflammation). (6)

Probiotics help eradicate bad bacteria by competing with them for adhesion sites, producing antimicrobial substances, and enhancing the immune response. (7)

Heal Your Gut, For Good

Taking care of your gut doesn’t have to be complicated. Once you understand what fuels a healthy gut and promotes good microbiome balance, you can make the daily choices to yield life-long, sustainable results.


What are the long-term dangers of bad gut bacteria?

Long-term dangers of bad gut bacteria include the development of autoimmune conditions, deteriorating mental health, constipation, fatigue, food sensitivities, headaches, hormone imbalances, joint pain, nutrient deficiencies, skin problems, and weight loss resistance.

What’s the difference between good and bad bacteria in the gut?

Good bacteria, also known as commensal bacteria, help maintain a healthy balance in your gut by aiding digestion, producing vitamins, and regulating your immune system. Bad bacteria, or pathogenic strains, produce toxins, cause infections, and disrupt the balance of your microbiome.

Every gut has both of these bacteria present (unless you’ve recently taken an antibiotic), but a healthy gut has a balance of bacteria that allows the commensal strains to crowd out pathogenic ones that begin to overgrow.

How do I know if I have SIBO?

Small Intestinal Bacterial Overgrowth (SIBO) requires a different approach to gut health. Symptoms of SIBO can include bloating, gas, diarrhea, and constipation. If you suspect you have SIBO, it's crucial to get tested, as probiotics might make the problem worse, not better.

Should you take probiotics with antibiotics?

Yes, taking probiotics with antibiotics can help maintain a healthy balance of gut bacteria, reducing the risk of antibiotic-associated diarrhea and other digestive disturbances by replenishing beneficial bacteria that antibiotics may destroy. (8)

How do you flush bad bacteria from your gut?

Flushing bad bacteria from your gut can be achieved by consuming a diet rich in fiber, fermented foods, and natural antibacterials like garlic and ginger while staying hydrated to help move and eliminate toxins and waste.


  1. Hamaker, B. R., & Tuncil, Y. E. (2014). A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota. Journal of molecular biology, 426(23), 3838-3850.

  2. Selvaraj, S. M., Wong, S. H., Ser, H. L., & Lee, L. H. (2020). Role of low FODMAP diet and probiotics on gut microbiome in irritable bowel syndrome (IBS). Progress In Microbes & Molecular Biology, 3(1).

  3. Bayan, L., Koulivand, P. H., & Gorji, A. (2014). Garlic: a review of potential therapeutic effects. Avicenna journal of phytomedicine, 4(1), 1.

  4. Sorrenti, V., Ali, S., Mancin, L., Davinelli, S., Paoli, A., & Scapagnini, G. (2020). Cocoa polyphenols and gut microbiota interplay: bioavailability, prebiotic effect, and impact on human health. Nutrients, 12(7), 1908.

  5. Ortiz-Alvarez, L., Xu, H., & Martinez-Tellez, B. (2020). Influence of exercise on the human gut microbiota of healthy adults: a systematic review. Clinical and translational gastroenterology, 11(2), e00126.

  6. Shi, X., Zhang, J., Mo, L., Shi, J., Qin, M., & Huang, X. (2019). Efficacy and safety of probiotics in eradicating Helicobacter pylori: A network meta-analysis. Medicine, 98(15), e15180.

  7. Wang, F., Feng, J., Chen, P., Liu, X., Ma, M., Zhou, R., ... & Zhao, Q. (2017). Probiotics in Helicobacter pylori eradication therapy: Systematic review and network meta-analysis. Clinics and Research in Hepatology and Gastroenterology, 41(4), 466-475.

  8. Ramirez, J., Guarner, F., Bustos Fernandez, L., Maruy, A., Sdepanian, V. L., & Cohen, H. (2020). Antibiotics as major disruptors of gut microbiota. Frontiers in cellular and infection microbiology, 10, 572912.


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