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How to Heal your SIBO Holistically

I am two months into my holistic protocol to rid of the Small Intestinal Bacterial Overgrowth (SIBO) that I was recently diagnosed with. This holistic approach, involving herbal antimicrobials, diet, and lifestyle changes is the first of three phases to heal my gut.

In my last post, I talk about what exactly SIBO is and the signs and symptoms that pointed towards SIBO being a major cause of my digestive issues. Now, let's break down how to heal from it!

3 Steps to Healing your SIBO

I am working with a naturopath to take a broad-spectrum approach to my healing. We are using a three-pronged approach to not only get rid of my SIBO, but also support my gut microbiome.

  1. Kill Phase

  2. Repair Phase

  3. Replenish Phase

More on phase two and three later. For now, it’s time to get rid of these pesky bacteria taking over my gut microbiome.

Antibiotics v. Antimicrobials: Which is Right for Me?

When choosing the path to kill off your SIBO, you need to address a simple question: What is my health goal?

Are you looking to rid of the SIBO as quick as you can and have a nice chunk of change to spend on antibiotics? Go the antibiotic route!

If you have the time to heal, want to spend less money, and don’t want to go back to antibiotics (if they are one of your root causes for gut issues), go with antimicrobials.

Studies show that antimicrobials are as effective (if not better!) than antibiotics. Antimicrobials can include a combination of herbs like wormwood, neem, oregano, berberine, and allicin. These herbs are known to rid of bacteria and pathogens within your gut.

Similar to antibiotics, antimicrobials will kill just about everything in your gut. That’s why it’s important to follow a replenish and repair phase with either route you choose.

Antibiotics are, traditionally, the most popular way to rid of SIBO. Typically, an antibiotic like rifaximin is prescribed for all types of SIBO. You can start to feel the effects within a couple of weeks, and your digestive issues may even completely go away! So, it’s a quick way to rid of SIBO.

The drawbacks of antibiotics are…they are antibiotics. Which is a primary cause of gut issues for a lot of people! It will kill off all of the good, the bad, and the ugly bacteria you have. It’s not a bad approach, but if you are trying to heal your chronic gut issues, and a weakened immune system could be a root cause, perhaps antibiotics are not the way to go.

Antibiotics can also be quite costly if you do not have health insurance. Even with health insurance, rifaximin can run $3,000.

If you are seeking a more holistic approach, you can turn to the herbal route.

The herbal route involves different antimicrobials, typically in the form of supplements, to rid of the bad bacteria in your gut.

These supplements typically are not covered by insurance. But they only cost about $120 for a 30-day supply.

This approach can take longer for your symptoms to go away. I have to say I am two months into the herbal route, and still feel like I am going through a lot of die-off symptoms.

It can take about 8-12 weeks to completely rid of your SIBO with antimicrobials. It will also involve trial and error, as you find the correct dosage for you.

You will also want to be cautious of how long you are taking antimicrobials. Microbes can become resistance to any remedy, antimicrobials or antibiotics. Switching between different types and the dosage of antimicrobial supplements can help you overcome SIBO.

So, when deciding which route to go, there is no right answer! I will say that working with a naturopath, they typically cannot prescribe medication (at least in the state of New York they cannot). In that case, you may have to work with a gastrologist or primary care doctor for this prescription.

The Antimicrobial Protocol My Naturopath Prescribed for SIBO

I have ventured for the antimicrobial route because if I am healing my gut, I want to feel like I am doing it the right way. A weakened immune system and depleted gut microbiome from chronic antibiotic use is one of the root causes of my gut dysbiosis and SIBO. If I don't have to put my body through a round of antibiotics, I don't want to!

Plus, I don’t have three grand to drop on antibiotics.

Here is the exact protocol I am following for Phase 1: The Kill Phase

For the record, I am not a certified doctor or naturopath. The protocol listed below is unique to me and my diagnosis. I hope by sharing my journey, it empowers you to take the next steps on your healing journey!

  • SIBOtic – 3 capsules twice per day with lunch and dinner for an antimicrobial agent*

*swapped this broad-spectrum antimicrobial for Para Biotic Plus, as SIBOtic was too strong and was making me feel nauseous. I am taking 3 capsules twice per day after lunch and dinner.

  • GI Microb-X – 1 capsule once per day in the morning as an antimicrobial agent*

*experimented with increasing the dose and it caused more diarrhea/looser stool. The Berberine Sulfite in this has caused diarrhea in the past for me, so be aware of that if trying berberine!

  • Motility PRO – 1 capsule once per day in the morning as a prokinetic help with GI motility throughout the day

  • Activated Charcoal – 2 capsules at night (away from other supplements!) for additional support and help with die-off symptoms.

Dietary Changes for SIBO Protocol

After the elimination diet, I learned that I am intolerant to gluten, dairy, soy and corn. I am going to keep these food groups out of my diet during the kill stage and am planning to slowly reincorporate them after my gut is healed!

About a month into my SIBO protocol, I also learned that I may be sensitive to fiber. People diagnosed with SIBO can have a hard time digesting both soluble and insoluble fibers. Fiber is crucial for our diets, but too much of it may be exacerbating your symptoms (which is why I fume when I hear the tip “just eat more fiber! ugh).

So, my meals are centered around a lower fiber, high protein, and high fat diet.

  • Breakfast – For a high protein and healthy fat-rich breakfast, I’ll go for sourdough bread (which has a low gluten index, and can be tolerated by people who have a gluten intolerance), avocado, eggs, and berries

  • Lunch/Dinner – ½ plate with cooked veggies (beets, tomatoes, cucumber, spinach, asparagus, artichokes, green beans etc.) ¼ with protein, ¼ complex carbs like sweet potatoes. Use oil to garnish.

  • Mealtime – To help my digestive system clean and repair in between meals, I am going to stick with breakfast, lunch, and dinner and avoid snacking. I will also try to eat meals around the same time each day.

Everybody’s body is different! Some people do great on the Low FODMAP diet, others can tolerate more food than what’s on that list. It’s helpful to do the elimination diet to see what you can tolerate.

The last thing you want to do is be on a super restrictive diet for too long. Many of the SIBO diets like low FODMAP and Specific Carbohydrate Diet (SCD) are meant to be temporary. 1-2 months at a time.

Try your best to eliminate foods that are known to causing your flare-ups, but also ensure you are having a bowel movement everyday. That’s why supplements, like magnesium citrate, can help with bowel movements, because sometimes diet alone won’t cut it!

Lifestyle Changes for SIBO Protocol

  • Aloe Vera Juice – I will continue to drink aloe vera juice daily to help with gut motility.

  • Probiotics – At first, I was continuing to eat probiotic rich foods, like saurefraut, kinchi, and kombucha. But I found that probiotics and fermented foods flared up my symptoms, causing severe bloating and nausea. I would recommend experimenting with probiotics during this time and see if your body can tolerate it or not during the "kill" phase.

  • Sleep – During any type of “kill phase” quality sleep is crucial! The bacteria is going to hate that it’s dying off, so you’ll need your immune system to perform it’s best! Quality sleep is key, and I find having a consistent nighttime routine helps with this.

  • Lymphatic drainage – Much like how sleep is beneficial, I need to ensure the detoxification pathways in my body are performing optimally. I will do lymphatic drainage massages through dry brushing, soaking in Epsom salt baths, and using a sauna 2-3 times a week.

  • Fasting – I will incorporate different length fasting (anywhere from 12-36 hours) during these next 8-12 weeks. This will help reset my gut microbiome, and keep my body in optimal health.

  • Herbal Teas – I will swap out caffeine for herbal teas as much as I can! I still love my morning coffee, but after 9AM, it’s time to switch over to herbal teas (hello, optimal sleep!). Additionally, teas like ginger will help ease any nausea and peppermint with help soothe my gut.


I hope learning of my protocol helps you on your healing journey. Going through this process is not easy, but if I had some guidance on what another woman was doing to heal, it could help me tremendously on my own path.

Would love to hear more about what you learned, or already know about SIBO, and your own experience around gut health!



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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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