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SIBO Repair Protocol: Essential Supplements, Diet, and Lifestyle Changes for Healing SIBO

After three months of antimicrobials to treat my SIBO and gut dysbiosis, it was time to move into phase two of my holistic healing protocol for SIBO: The Repair Phase.

In this next phase, it's all about supporting and maintaining your gut integrity. This looks like replenishing it with good, healthy bacteria and promoting microbial diversity within your gut. To help rebuild the integrity of your gut lining after antimicrobials or antibiotics, supplements, diet and lifestyle changes may be necessary!

We’ll review how to take charge of your gut health and overcome SIBO, exploring the essential supplements, diet adjustments, and lifestyle habits for effective healing.

As always, I provide full transparency into the unique protocol my naturopath created for me. Always consult your doctor/physician before you incorporate any diet or lifestyle changes. I am not a medical professional, but I hope this helps educates and empowers you on your own gut healing journey!

The Essential Supplements for SIBO Recovery

I had a whole new lineup of supplements that I started to incorporate after the round of antimicrobials. These supplements worked together to support the integrity of my gut lining, promote a healthy balance of bacteria in my gut, lower overall inflammation and support my immune function.

Motility Pro from Ortho Molecular Products - 1 capsule once per day in the morning (on an empty stomach).

I took this supplement to during my first phase of healing to stimulate gastric mobility. I brought in back into my health plan because it helps you to go if you know what I mean. The herbal blend promotes a healthy microbial balance in the GI tract and is perfect for those struggling with gut motility issues, SIBO, and chronic constipation.

Vital Nutrients Betaine HCL Pepsin and Gentian Root Extract - One capsule, three times daily before a meal.

Pure Encapsulations Pancreatic Enzyme Formula - One capsule, three times daily before a meal.

Omega-3 Fish Oil - 3 capsules, once a day with breakfast.

Vitamin D + K - 1 capsule, once a day with breakfast.

FemOne Women’s Multivitamin from Metabolic Maintenance - 1 capsule, once a day with breakfast.

VSL #3 Probiotic Medical Food - 2 capsules, once a day with breakfast.

Microbiome Labs Mega Mucosa Mucosal Support - Start with 3 capsules at night before bed for one week. If tolerated, increase to 6 capsules before bed.

A Look at my Current Diet

Since last November, I shifted my diet to limit starchy foods and sugar. Even after doing the elimination diet and removing gluten, dairy, soy, and corn, I was still experiencing pretty significant digestive issues. And since I was pretty symptomatic after three months of antimicrobials, the only thing to do was change my diet once more.

By removing starches, like rice, potatoes, oatmeal, and sourdough, and sugars, like added sugar and fruit, we were trying to starve off any lingering bacteria/yeast that may still be present. I also removed chicken and corn, since it’s difficult to find pasture-raised chickens that do not feed off of soy and corn (things that I am intolerant to).

Overall, I removed:

  • gluten

  • dairy

  • corn

  • soy

  • chicken

  • eggs

  • fruit

  • starches

Basically, I was a dairy-free keto girlie!

And honestly, it has been hell. As an avid foodie, I can’t really eat out and it’s been difficult to be inspired by my meals. I constantly remind myself why it’s important to stick to these limited diets: Short term sacrifices will lead to long-term healing. But I also needed to find balance over the holiday season for my own sanity.

One thing that kept me motivated is that I actually noticed a pretty significant change in my digestive issues when I switched my diet. I did a similar diet, the Candida Diet, last year to help with Candida Overgrowth and found it helped significantly. So, that’s another reason for removing starches/sugars. Even though my symptoms are not perfect (it still seems like I bloat pretty bad at the end of the day and am cyclically constipated), it is a world’s better than where I was at last May before I started working with my naturopath.

Now, I am slowly starting to reincorporate fruit, like berries, and starches into my diet. We are starting slow, with Congee (basically a rice porridge), and monitoring my symptoms.

I also decided to take another stool test. I ordered the GI Map through Direct Labs (sidenote, they do not ship directly NY, NJ, or RI because of state laws, so you will have to order to a relative or friend in another state first. Annoying, but it is what it is).

This will test a variety of things, including bacteria/yeast overgrowth, h. pylori, pancreatic function, estrogen metabolization and more.

I think it’s important to take stool tests frequently, especially as you are working through different protocols, and may still be experiencing symptoms. The last stool test I took that looked at the microbial makeup of my gut was over a year and a half ago. A lot has changed since then, so it’s good to get another look at what else could be awry.

Additionally, I opted into a food allergy test. I’m at a point where I am still symptomatic almost immediately after I eat. Even switching up my diet, I can still feel quite nauseous and bloated after a meal. Taking a food allergy test through Meridian Valley Lab will help test for 95 different foods, pinpointing the exact foods I should avoid. Because clearly, I feel like I’m missing something!

My Lifestyle Approach during the Repair Phase

While diet and supplements are important aspects to the repair phase, they would make little to no difference if I didn’t make some lifestyle changes, too! Here are some of my favorite habits I’ve picked up over the last six weeks that have made a huge difference.

  • Sleep: Sleep will forever be a number one habit I work to improve upon! It’s certainly not perfect, I have found with the holidays it’s difficult to maintain a consistent sleep schedule. Since the time we go to bed has a big impact on the biodiversity of our gut microbiome, I make a conscious effort to go to bed around the same time every night. Yes, that includes the weekends! Winding down around 10PM and aiming for 8-9 hours of sleep has me feeling my best self the next day and offers my body ample time to repair during the night.

  • Castor Oil Packs: I started incorporating these in October during the first phase of my healing protocol, but they deserve more recognition! I ordered a castor oil pack + castor oil from Amazon and use the packs on my stomach five to six nights a week. The castor oil is able to penetrate deeper into your tissues, stimulating your GI tract and cleanse the body. It’s the only way I can wake up not feeling bloated!

  • Bone Broth: This is something I’ve been incorporating in my diet for a while to help support my gut lining. It’s amazing at healing intestinal permeability (aka Leaky Gut) and reducing inflammation from a damaged gut. I try to aim for at least one cup a day, but I have been able to incorporate more by cooking with bone broth and using an L-Glutamine supplement from Throne (which is the main component of bone broth).

  • Removing Smoothies/Cold Drinks/Raw Foods: I’ve noticed a significant reduction in nausea after a meal by taking out smoothies, cold drinks (sad day for my iced latte days) and raw foods. I break down the benefits of incorporating warming foods for gut health in this post.

  • Lemon Water with Himalayan Salt in the morning: I feel like this one is silly to do and idk if it’s placebo at this point, but I’m hooked. I add fresh lemon juice to hot water and a pinch of sea salt right when I wake up. The minerals from the salt and lemon not only hydrate me, but the warm water flushes toxins out my body. It’s an easy hack to get me drink water first thing in the morning (not a girlie who can chug a liter of water when she wakes up) and combined with motility pro, really helps me to go in the AM.

  • Yoga Tune Up Balls: I am obsessed with this yoga tune up ball! Such a simple concept to use on the balls of your feet or any point you feel tense (like between your shoulder blades). It’s a massage tool with precision rolling to help disperse pressure and destress you. I find myself using it consistently, like when I’m brushing my teeth, answering emails, or laying down for a meditation. 10/10!!!

  • Non-Sleep Deep Rest: This is a new concept for me I started to incorporate a couple of weeks ago. It is a Yoga Nidra practice that is regenerative and healing. When I start to experience that afternoon crash, doing even just 10 minutes of NSDR helps to relax my body in a way that feels like I just slept for 8 hours. It has been mind-blowing, and a habit I want to continue to build upon!


So that is about it for now! I will keep you posted when I move to phase three: The Repair Phase, and the results of any tests I take.

Leave a comment if you have any questions, or if you have any recommendations for supplements, diet, and lifestyle changes!🌿



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Welcome! If you made it here, you are probably looking for answers on where to begin your wellness journey. I'm Jessica, and I started my gut health journey over 3 years ago. As an avid foodie and wellness enthusiast, I hope to inspire you on your realistic wellness journey.

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