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

As a functional medicine expert, it is my mission to educate my patients and readers like you on how to starve out the bad gut bacteria while increasing good bacteria in your gut ecosystem.

Read on for my step-by-step guide to learn exactly how to create an ideal microbiome for your healthiest self. Each step builds upon itself for the sake of long-term gut health. Let’s dive in!

LISTEN: The Gut-Brain Connection, How Probiotics Actually Work, The Best Bacteria Strains For Your Microbiome + The Game-Changing Power Of Mindfulness To Elevate Your Mood With Tina Anderson | Dr. Will Cole

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.

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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.

READ NEXT: Leaky Gut Diet: Food That Heals + What To Avoid

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!