How to Heal Your Gut in 5 Steps

How To Heal Your Gut in Perimenopause & Menopause

Here’s something you may not know.

All disease begins in the gut. More than 2,000 years ago, Hippocrates stated this, and research confirms that he was definitely onto something.

While all disease doesn’t literally start in the gut, many metabolic, autoimmune, and cognitive diseases do in fact start with gastrointestinal disturbances or imbalances. These findings highlight that you cannot achieve optimal health without a healthy gut. The gut, which includes everything from your mouth to your anus, hosts trillions of bacteria, fungi, and other organisms. It also houses 2/3 of your immune system, the majority of neurotransmitter production, influences your metabolism, contributes to energy homeostasis, and so much more.

People incorrectly assume that an absence of GI symptoms means a healthy gut, but that is far from true. While digestive symptoms such as bloating, gas, constipation, diarrhea, abdominal pain, etc., are very common, it’s also almost as common for symptoms to present neurologically. Gut disturbances often result in symptoms such as brain fog, poor concentration, poor memory, depression, and anxiety. This is because the gut and the brain are in constant communication via the gut-brain axis. Poor gut function can lead to poor brain function. Other areas closely affected by the gut include the skin, the immune system (and risk of autoimmune disease), blood sugar regulation, detoxification, and metabolism/mitochondria.

Let’s heal your gut! 

Whether you are dealing with digestion issues, autoimmunity, brain fog, fatigue, or skin issues, the 5R gut healing protocol could be hugely helpful. When gut health is compromised, there’s no quick fix and a specific order of operations as healing progresses. That’s where the 5 Rs come in!

What is the 5R Gut Healing Protocol?

The 5R gut healing protocol restores the natural balance of your gastrointestinal tract. Because many of us are exposed to environmental toxins, crappy diets, and daily stress, our gut health has a high likelihood of being less than optimal. The result is the issues mentioned above, in addition to hormone imbalance. And if you’re in perimenopause or menopause, you don’t need that! 

The 5R protocol focuses on five parts to restore your natural gut balance, including:

  • Remove
  • Replace
  • Repopulate
  • Repair
  • Rebalance


The first step in gut healing involves removing all the bad actors that are causing your gut to revolt. Continued exposure to these insults will result in continuing problems. These may include:


Food sensitivities are a major drawback to gut health. The problem is that many people don’t know they have any! Food sensitivities can cause various symptoms, including but not limited to: headaches, acne, joint pain, constipation, and anxiety. 

Some of the most common sensitivities are from gluten, dairy, soy, and eggs, but every person’s body is unique. To know which foods you are sensitive to, you can try an elimination diet of likely offenders or get a food sensitivity test performed. It’s better to test than to guess if you want the best results.

Infections, Pathogens, Bacteria, and Parasites

These issues show up on a stool test, and you should eliminate them ASAP. You can’t truly heal if your gut constantly battles these foreign invaders. There are different protocols to remove yeast, parasites, and pathogenic bacteria. 


Stress weakens your intestinal lining, allowing gut bacteria to enter your circulation… where you do not want them! Managing stress is challenging at best but doable. Start by identifying your sources of stress and changing what you can. Breathwork, exercise, getting out in nature, prayer, meditation, and scheduling a bit of downtime for yourself are all helpful. All of these are PRACTICES, so don’t expect perfection. That increases stress!


Toxins in your water, food, and home and beauty products can disrupt your microbiome, killing off the helpful bacteria. When your body is exposed to toxins daily, they build up in your body if your detoxification pathways are not optimized. These toxins can disrupt the gut’s normal functioning, leading to chronic diseases, allergies, obesity, and other GI issues. 


Next, you’ll want to replace missing elements vital to digestion. These can include replacing digestive enzymes, betaine HCL, and ox bile. Ox bile or bile acids are critical in digestion since they increase the absorption of fat-soluble vitamins. To replace these, you can use supplementation specific to your body’s needs.

You can also eat foods stimulating stomach acid and digestive enzymes such as bitters. These supplements help your body break down fats, carbohydrates, and proteins more effectively. Another reason why having an adequate amount of bile is critical is because it plays a role in toxin elimination. Bile is how many dangerous “fat-loving” substances and toxins get excreted from the body. It also has some antimicrobial properties to help keep gut bacteria balanced.


Good bacteria in your gut may get crowded out by opportunistic bacteria or killed off by drugs like antibiotics. Getting these back in balance can be accomplished with fermented foods or probiotic supplements. Prebiotics are also essential to help feed the good bacteria. Here’s a list of foods that have prebiotic properties


Fixing your damaged gut is essential for long-term gut health. You need to repair your gut lining, mucosa, and damage from inflammation. You’ll want to include more vitamins A, C, E, and D, zinc, collagen, and amino acids, particularly L-glutamine. Some herbs like marshmallow root, slippery elm, and aloe vera are soothing to the gut. Bone broth is excellent for gut repair, but if you have histamine reactions, you should avoid it.


The 5R protocol will only be successful long-term if you don’t return to your old ways of living. To truly rebalance your gut, consider your lifestyle behaviors. For example, using NSAIDs like ibuprofen can be detrimental to your health when they are unnecessary. Rebalancing requires rooting around all corners of your life for sources of poor gut health.

Bottom Line

Healing your gut isn’t a quick fix or fad. That’s why my Healthy Gut program is six months long! It takes effort and occasionally some trial and error. Lifestyle change is hard, but with support and accountability, the payoff of feeling amazing is worth it. 

Dr. Anna Garrett is a menopause expert and Doctor of Pharmacy. She helps women who are struggling with symptoms of perimenopause and menopause find natural hormone-balancing solutions so they can rock their mojo through midlife and beyond. Dr. Anna is the author of Perimenopause: The Savvy Sister’s Guide to Hormone Harmony. Order your copy at

Also, she offers a membership group, Hormone Harmony with Dr. Anna Garrett, which provides women in midlife with affordable expert guidance and community support.

Dr. Anna is available for 1-1 consultation. Find out more at

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Perimenopause: The Savvy Sister’s Guide to Hormone Harmony

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