Taking Care of Your Gut

Simple Steps for a Healthy Microbiome

Taking care of your gut doesn’t have to be complicated. While there’s a lot of talk about specialized protocols, the truth is that simple, consistent steps can go a long way in supporting a healthy microbiome. While some may benefit from working with a specialist, there’s a lot you can do independently to set the stage for better gut health.

Healing the gut is about working with the body, not against it. A well-tended gut doesn’t just function better—it increases overall resilience, making it easier to tolerate potential disruptors. The goal isn’t to live in fear of everything that might harm your gut, but to build a strong foundation that allows for flexibility and adaptability.

Here’s a straightforward approach to gut health, broken down into three key steps:

1. Pathogen Control – Keeping harmful bacteria, fungal overgrowth, and other pathogens in check without disrupting the balance of beneficial microbes.
   

2. Tending the Gut Lining – Using gentle, nourishing herbs to help repair and protect the digestive tract.
   

3. Repopulation – Introducing probiotics and prebiotics at the right time to support a thriving gut ecosystem.
   

Personal responsibility plays a big role in gut health. Supporting the microbiome means making choices that align with this protocol—such as avoiding unnecessary medications like Tylenol, reducing pesticide exposure, and addressing food intolerances. While the body is adaptable, consistently working against gut health can make the healing process harder.

The Foundations of Gut Health

Before diving into the protocol, certain foundational habits can help set the stage for gut resilience. These habits are essential during all stages of the protocol and in everyday life for long-term gut health:

• Support Healthy Stomach Acid Levels – Stomach acid is essential for digestion and keeping harmful bacteria at bay. Taking bitters before meals (or eating bitter foods), consuming enzyme-rich foods like avocado, and avoiding excessive water intake during meals can help maintain strong acid levels.
  

• Keep Detox Pathways Flowing – Regular bowel movements, sweating, and lymphatic support are key to removing waste and maintaining a healthy gut. Hydration, movement, and liver/lymph-supporting herbs can help keep detox pathways open.
  

• Reduce Gut Disruptors – Avoid excessive antibiotic use, unnecessary medications, pesticides, and highly processed foods to make it easier to maintain gut balance.
  

• Prioritize Nutrient-Dense Foods – Whole, unprocessed foods provide the nutrients the gut needs to repair and thrive. Bonus points if they’re rich in antioxidants or prebiotics!
  

These habits help create a stable foundation so that any gut-healing efforts are more effective.

Step 1: Pathogen Control

Most people have some level of gut imbalance, whether it’s bacterial overgrowth, candida, or just a lack of beneficial microbes. Before focusing on rebuilding, it helps to gently clear out the things that don’t belong. If your detox pathways are sluggish, addressing this first may be necessary. Signs of sluggish detox pathways can include fatigue, brain fog, skin issues, slow digestion, and heightened reactions to supplements or foods.

When the body is ready for pathogen control, short-term use (2-4 weeks) of antibacterial, antifungal, and antiparasitic herbs can help keep things balanced. Below is a list of effective herbs, ordered from strongest to mildest:

• Stronger Herbs (Best for Short-Term Use)
  

• Black Walnut – A powerful antiparasitic and antifungal that helps eliminate intestinal invaders. Use cautiously, not for extended periods.
  

• Wormwood – A traditional antiparasitic that works well for gut infections but should not be used during pregnancy.
  

• Clove – Known for its ability to kill parasitic eggs and support microbial balance.
  

• Pau d’Arco – An antifungal and antibacterial herb that helps with candida overgrowth and gut dysbiosis.
  

• Moderate Strength Herbs (Great for a protocol and/or longer-term use)
  

• Usnea – A natural antibiotic that supports the immune system and helps address stubborn infections.
  

• Elecampane – Supports lung and gut health by clearing excess mucus and fighting bacterial infections.
  

• Olive Leaf – A broad-spectrum antimicrobial that supports the immune system and fights bacteria, viruses, and fungi.
  

• Wild Bergamot – Gently supports microbial balance while calming gut irritation.
  

• Yarrow – Supports digestion, regulates gut bacteria, and has mild antimicrobial effects.
  

• Milder Herbs (Great for daily use or when pregnant)
  

• Honeysuckle – A cooling antimicrobial useful for gut infections accompanied by inflammation.
  

• Garlic – A well-known antimicrobial with broad-spectrum action that supports gut and immune health.
  

• Oregano (not oregano oil) – A culinary herb that helps regulate gut bacteria and has antifungal properties.
  

• Chinese Skullcap – Supports bad bacteria while easing symptoms of leaky gut and reducing inflammation.
  

To avoid detox symptoms, consider using activated charcoal, bentonite clay, or diatomaceous earth to bind and remove waste without burdening the system.

Step 2: Healing the Gut Lining

Healing the gut lining is the longest part of the protocol and can be done alongside the other steps. It’s an ongoing process that doesn’t stop once healing is achieved. Regularly consuming gut-supportive herbs and foods will help maintain gut integrity long-term.

The gut lining takes a hit from modern diets, environmental toxins, and medications. When compromised, toxins and inflammation markers can leak into the bloodstream, contributing to autoimmune issues and nervous system dysfunction.

Here are some tried-and-true gut healers:

• Comfrey Leaf, Calendula, Plantain – Strengthen and restore tissue (best used in infusion form).
  

• Marshmallow Root/Leaf, Slippery Elm Bark – Demulcent herbs that coat and protect the gut lining (best in cold infusion).
  

• Meat Stock and Bone Broth – Meat stock is gentler in the early stages; bone broth can be introduced once the gut is stronger.
  

• Fulvic Acid – A mineral-rich compound that supports gut health and nutrient absorption.
  

Incorporating these herbs and foods long-term will help maintain gut resilience. It generally takes 6-8 months for the gut lining to fully rebuild, so patience is key.

Step 3: Repopulation

When repopulating the gut, variety is key. Taking the same probiotic supplement with just a few strains indefinitely can actually reduce microbial diversity over time. A more diverse microbiome leads to greater resilience, so incorporating a variety of probiotic sources ensures a well-balanced gut ecosystem.

Effective ways to support repopulation:

• Prebiotics – Foods and herbs that feed good bacteria, such as dandelion root, chicory root, and burdock root.
  

• Spore-Based Probiotics – Probiotics that act as “seeds” that colonize the entire digestive tract (e.g., Megaspore).
  

• Saccharomyces Boulardii – A beneficial yeast that helps regulate gut flora, particularly after antibiotic use.
  

• Fermented Foods – Sauerkraut, kimchi, kombucha, or coconut water kefir (for those sensitive to histamines, coconut water kefir can be gentler).
  

• Time Outdoors – Spending time in nature naturally increases gut bacterial diversity, so get outside!
  

Gut health doesn’t have to be overwhelming. Small, consistent efforts can make a big difference. The key is to listen to your body, take it step by step, and trust in the process. Your gut will thank you!