Gut Health & The Microbiome: How To Heal Your Gut
If you’ve been struggling with bloating, fatigue, or stubborn weight loss, improving your gut health may be the solution you’ve been missing.
Your gut is more than just a place where food is digested—it’s the command center for your health, energy, mood, and longevity. Scientists call it the “second brain”, and with good reason: your gut microbiome (the trillions of bacteria, fungi, and microorganisms living in your intestines) affects everything from weight management and hormone balance to mental clarity and disease prevention.
You are going to learn about gut health basics, the power of fermented foods, and simple steps to strengthen your microbiome for better energy and wellness.
This post will give you the science-backed knowledge and practical tools you need to improve your gut health—from the right foods and recipes to supplements and daily habits—so you can feel energized, balanced, and in control of your wellness.
Taking care of your gut isn’t a wellness trend—it’s a science-backed strategy for long-term health.
This post is all about gut health & the microbiome: How to heal your gut.
Why Taking Care of Your Gut Health Matters
Most people think of gut health only in terms of digestion, but your microbiome is like a control center for your entire body. Here’s why it deserves your full attention:
- Immune System Powerhouse: Nearly 70% of your immune system lives in your gut. A healthy microbiome helps your body recognize harmful invaders, reduce chronic inflammation, and strengthen your natural defenses.
- Weight, Metabolism & Hormones: Research shows your gut bacteria can influence how efficiently you burn calories and store fat. Dr. Layne Norton emphasizes that without enough fiber and a balanced gut environment, even the best diet won’t deliver sustainable results.
- Mood & Mental Health: The gut produces about 90% of your serotonin, the “feel-good” neurotransmitter. A healthy gut can lower your risk of anxiety, depression, and brain fog. This is why it’s often called the “second brain.”
- Energy & Nutrient Absorption: A thriving microbiome makes it easier to absorb vitamins, minerals, and amino acids from food, fueling your muscles, brain, and metabolism. Dr. Gabrielle Lyon notes this is especially important for women over 30 who want to preserve muscle and energy as they age.
- Longevity & Disease Prevention: Studies connect poor gut health with higher risks of autoimmune disorders, obesity, diabetes, and even Alzheimer’s. Supporting your gut with the right foods and habits isn’t just about feeling good today—it’s about protecting your health for the future.
gut-healthy foods
“Fiber is the most underrated superfood—it feeds your gut bacteria, lowers inflammation, and supports everything from weight management to longevity.” — Dr. Mark Hyman
Fiber, Probiotics, and Prebiotics: The Foundation
If you want a healthier gut, you need to give your microbiome the right fuel and reinforcements. Think of fiber, probiotics, and prebiotics as the three pillars that support everything else.
Fiber: Your Gut’s Favorite Food
Fiber isn’t digested by you—it’s digested by the trillions of microbes in your gut. This process produces short-chain fatty acids (SCFAs), like butyrate, which reduce inflammation, protect your colon lining, and support metabolism.
- Daily target: 25–35 grams per day (most people only get 10–15g).
- Best sources: oats, lentils, chickpeas, leafy greens, flaxseeds, berries.
💫 Dr. Layne Norton consistently points out that fiber, alongside protein, is the most under-consumed but critical nutrient for health and body composition.
Prebiotics: Fuel for the Good Guys
Prebiotics are a type of fiber that specifically feeds the good bacteria. Without prebiotics, probiotics (the “good guys”) don’t survive as well in your gut.
- Examples: garlic, onions, leeks, asparagus, bananas, oats, Jerusalem artichokes.
- Benefit: more diversity in your gut microbiome = better digestion, mood regulation, and hormone balance.
Probiotics: Reinforcements for Your Microbiome
Probiotics are live bacteria that restore balance in your gut, especially helpful after antibiotics, illness, or digestive upset.
- Food sources: yogurt, kefir, sauerkraut, kimchi, miso, kombucha.
- Supplement tip: Choose a multi-strain probiotic with at least 10–30 billion CFUs for broad coverage.
💫 Dr. Mark Hyman often emphasizes that adding probiotic-rich foods is one of the easiest and most effective ways to boost gut diversity and immune resilience.
Gut-Healthy Foods You Should Eat Daily (and Why They Work)
It’s not just what you eat—it’s how those foods interact with your microbiome that matters. These gut-healthy staples don’t just fill your plate, they actively shape your digestion, immunity, and metabolism.
1. Oats, Barley, and Whole Grains
- What they do: Rich in soluble fiber (beta-glucan), whole grains act as prebiotics, feeding beneficial bacteria.
- How they help: When bacteria ferment these fibers, they produce short-chain fatty acids (SCFAs) like butyrate, which lower inflammation, strengthen the gut lining, and support metabolic health.
- Science says: A study in the British Journal of Nutrition found that whole-grain intake increases microbial diversity, a marker of a healthy gut.
2. Lentils, Beans, and Chickpeas
- What they do: Packed with resistant starch and fermentable fiber.
- How they help: These starches bypass digestion in the small intestine, reaching the colon where gut bacteria ferment them into SCFAs—fuel for your colon cells and protectors against colon cancer.
- Science says: Dr. Donald Layman notes that pairing legumes with protein improves satiety while also supporting gut microbiome diversity.
3. Leafy Greens (Spinach, Kale, Arugula)
- What they do: Contain a unique sugar molecule called sulfoquinovose (SQ) that feeds beneficial bacteria.
- How they help: Promote growth of bacteria linked to reduced gut inflammation.
- Science says: Research from the Journal of Nature Chemical Biology showed that SQ sugars from leafy greens play a key role in fueling protective gut microbes.
4. Berries (Blueberries, Raspberries, Blackberries)
- What they do: Loaded with polyphenols and soluble fiber.
- How they help: Polyphenols act as antioxidants and prebiotics—gut microbes metabolize them into compounds that lower inflammation and improve insulin sensitivity.
- Science says: Dr. Mark Hyman highlights polyphenols in berries as crucial for reducing oxidative stress and improving microbiome resilience.
Berry Good for Your Gut Health
Did you know that berries are one of the richest sources of polyphenols, plant compounds that your gut bacteria love to feed on? When these polyphenols are broken down, they help reduce gut inflammation and improve insulin sensitivity.
Fun fact: Blueberries have been shown to increase the abundance of beneficial bacteria like Lactobacillus in the gut, which play a role in immunity and digestion.
“Berries act like fertilizer for your microbiome—feeding the good bacteria that keep your gut, metabolism, and immune system thriving.” — Dr. Mark Hyman
5. Nuts & Seeds (Chia, Flax, Pumpkin, Walnuts)
- What they do: Provide fiber, omega-3s, and polyphenols.
- How they help: Omega-3s reduce inflammation while fiber feeds beneficial bacteria. Seeds like flax and chia also form gels in the gut that slow digestion, balancing blood sugar.
- Science says: A Nutrients review linked nut consumption to increased abundance of butyrate-producing bacteria.
6. Garlic, Onions, and Leeks
- What they do: Contain inulin, a natural prebiotic fiber.
- How they help: Inulin specifically fuels Bifidobacteria, one of the most beneficial gut bacteria species. More bifidobacteria = stronger immune system and better digestion.
- Science says: Dr. Layne Norton emphasizes the synergy of prebiotic fibers with protein for body composition and gut health.
7. Fermented Foods (Sauerkraut, Kimchi, Miso, Kefir, Yogurt, Kombucha)
- What they do: Contain live probiotics that directly add beneficial bacteria to your gut.
- How they help: Rebalance your microbiome, increase microbial diversity, and improve nutrient absorption.
- Science says: Dr. Gabrielle Lyon stresses that daily probiotic foods support immunity, reduce bloating, and promote long-term metabolic health.
Why Sourdough Bread Is Different (and Better for Your Gut Health)
Not all bread is created equal—and sourdough is proof. What makes sourdough unique is its fermentation process, which transforms a simple loaf into a gut-friendly food.
1. The Fermentation Process
- Sourdough is made with a starter—a live culture of wild yeast and lactic acid bacteria.
- During fermentation, these microbes predigest parts of the dough:
- Gluten proteins are partially broken down, making sourdough easier to tolerate for people sensitive (though not celiac).
- Phytic acid (an anti-nutrient) in wheat is reduced, improving mineral absorption (zinc, magnesium, iron).
- Complex starches are broken down, which slows digestion and prevents blood sugar spikes.
💫 Dr. Mark Hyman notes that this microbial action is what makes sourdough a true “functional food” compared to processed bread.
2. Benefits for the Gut Microbiome
- Natural Probiotics (During Fermentation): While most probiotics don’t survive baking heat, the fermentation process leaves behind metabolites that act like prebiotics, feeding beneficial gut bacteria.
- Postbiotics: The lactic acid bacteria in sourdough produce compounds that support microbial diversity and lower gut inflammation, even after baking.
- Lower Glycemic Impact: Studies show sourdough has a lower glycemic index than conventional bread, meaning steadier energy and less stress on insulin.
3. Why Store-Bought Bread Doesn’t Compare
- Commercial breads are often rushed through production with baker’s yeast, skipping fermentation.
- Many contain additives, preservatives, and emulsifiers that can disrupt the gut lining and microbiome.
- Without fermentation, gluten and phytic acid remain intact, making nutrients harder to absorb and digestion more stressful.
💫 As Dr. Layne Norton emphasizes, it’s not just about calories—it’s about how food quality impacts digestion and metabolism.
4. Sourdough = A True Gut-Supportive Carb
- Easier to digest.
- Supports microbial balance.
- Promotes better nutrient absorption.
- Provides steadier energy compared to highly processed bread.
The Gut-Brain Connection
Your gut and brain talk constantly via the vagus nerve. An unhealthy gut can trigger inflammation that influences mood, focus, and even depression risk.
- 90% of serotonin (your “feel-good” neurotransmitter) is made in the gut.
- A balanced microbiome = better stress resilience, mental energy, and sleep.
The Benefits of Fermented Foods
- Restore beneficial bacteria after antibiotics
- Reduce bloating and digestive issues
- Enhance immune system regulation
- Support hormonal balance through improved nutrient absorption
Dr. Donald Layman emphasizes that gut-friendly foods paired with adequate protein intake amplify metabolic health and longevity.
Simple Gut-Healthy Recipes
1. Fiber-Packed Berry Chia Pudding
- 3 tbsp chia seeds
- 1 cup unsweetened almond milk
- ½ cup mixed berries
- 1 tsp ground flax
- Dash of cinnamon
💫 Loaded with fiber, omega-3s, and prebiotics.
2. Sourdough Avocado Smash
- 1 slice of sourdough bread
- ½ avocado mashed with lemon juice
- Sprinkle of hemp seeds
💫 A mix of healthy fats + fermented fiber.
3. Gut-Healing Fermented Bowl
- ½ cup quinoa
- 1 cup sautéed greens
- ½ cup roasted chickpeas
- 2 tbsp sauerkraut
- Tahini drizzle
💫 Combines prebiotics, probiotics, and fiber.
What Supplements Help Gut Health?
- Probiotic supplement (multi-strain, 10–30 billion CFUs)
- Prebiotic fiber powder (inulin, partially hydrolyzed guar gum)
- Digestive enzymes (if you struggle with bloating)
- Glutamine (shown to improve gut lining integrity)
- Vitamin D (low levels are linked to poor gut microbiome diversity—Dr. Lyon emphasizes this for metabolic health)
Other Ways to Improve Your Gut
- Exercise regularly: Boosts gut microbial diversity.
- Sleep well: Poor sleep = gut dysbiosis.
- Stress management: Meditation, journaling, and breathwork protect the gut-brain axis.
- Limit artificial sweeteners: They can negatively alter gut bacteria.
References
- Lyon, G. (2023). Forever Strong: A New, Science-Based Strategy for Aging Well.
- Layman, D. K. (2003). The Role of Leucine in Weight Loss Diets and Glucose Homeostasis. Journal of Nutrition.
- Norton, L. (2022). Science-Based Nutrition & Training Principles. Biolayne Research.
- Hyman, M. (2021). Food Fix: How to Save Our Health, Our Economy, Our Communities, and Our Planet.
- Sonnenburg, J., & Sonnenburg, E. (2015). The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health.
This post was all about your gut health. It is a cornerstone of whole-body health. By eating more fiber, embracing fermented foods, and supplementing wisely, you can improve digestion, boost energy, balance hormones, and support your mental health.
As Dr. Layne Norton says: “If you want to optimize your health and longevity, start with the basics—protein, fiber, and movement. Your gut microbiome will thank you.”
