You’ve recently gotten the diagnosis: Your bloating, excess gas, constipation/diarrhea and heartburn/reflux are Small Intestinal Bacterial Overgrowth. You’ve done the breath test, and found that you either have a hydrogen or a methane positivity, and you’re wondering what to do next. But your diagnosis doesn’t have to be overwhelming or stressful—we can treat SIBO in a natural way, in two phases.

Our General SIBO Treatment Strategy

The two gases you were likely tested for are methane and hydrogen. They can cause different symptoms in each person. In general, methane positive SIBO is harder to kill than hydrogen positive bacteria, so when we are determining a treatment length for our two phases, we increase the number of months for patients with methane positive results.

PHASE 1: Starve the Bacteria

Day 1—7 of SIBO Treatment

To begin, we add in powerful herbal antimicrobials that help to eliminate the bacterial overgrowth. We use herbs, but there are conventional prescription antibiotics that have been researched for SIBO elimination, if you choose to go that route. We’ve found the herbs often work well enough that we can leave antibiotics as a last resort for more recurrent or stubborn cases.

We actually ask that patients continue eating their current, normal diet for a week while we start antimicrobial treatment. By eating normally, without restrictions, we encourage the bacteria to grow while we begin to kill them off with herbal antimicrobials. After 7 days, we have you start the dietary component.

Day 8

At this time we introduce the SIBO Specific Diet, created by Dr. Allison Siebecker, ND, which combines a specific carbohydrate diet (SCD) with low FODMAP foods. It’s based on the idea that we remove any foods that the SIBO bacteria could “ferment,” which is what typically causes SIBO symptoms. The bacterial is essentially starved, because they have nothing to feed on, which, paired with our herbal antimicrobials, means we’re both killing and starving them.

With severe cases of SIBO, we also recommend that you eat all your meals during the day, and make sure that you have a 12-hour fast overnight—this is when your gut nerves are at their most active. By fasting, you’re decreasing their workload, and allowing them to heal (see more about healing the gut nerves below).

The SIBO Specific diet is a therapeutic diet only, and not intended to be done long term. We recommend working with a registered dietitian to help guide you through the SIBO Specific Diet as it can be restrictive, and hard to navigate. If you’re also suffering with other diseases such as diabetes or are on medications that alter your blood sugar, you have other food intolerances, or you are vegan/vegetarian, the dietary piece can get really complicated, making a registered dietician a necessary part of your treatment plan.

A caution: Once you’ve started taking herbal antibiotics and begun a SIBO meal plan, the bacteria causing your SIBO will begin to die off. This can lead to a die off reaction, sometimes called a “detox reaction.” It can be hard to predict what your symptoms may be, but you might experience headaches, increased fatigue, worsening acne, rashes, reflux, or the feeling that you’re coming down with the flu or a cold. These don’t mean that the treatment isn’t working—in fact, it’s the opposite! Sometimes things get worse for a short period before your body can fully heal.

After your prescribed length of treatment time (which can vary, depending on whether you’re methane or hydrogen positive), we evaluate whether or not the SIBO is gone by doing a second breath test or adding in a food challenge (we test your symptoms as they relate to eating certain foods that can activate still existing SIBO).

PHASE 2: Heal Your Gut Nerves & Lining

In part 1 of our SIBO series, we talked a bit about how when gases start to intoxicate the nerves of the migrating motor complex (a.k.a. the nervous system of your gut), they can either speed it up or slow it way down. Either way, it can also cause a lot of inflammation and potentially some damage. So after all your SIBO bacteria is eradicated, we get into phase 2, which is healing the gut nervous system.

At this point, if we haven’t been working on the cause of your SIBO, we start to do that now. (Why wouldn’t we have been working on the cause all along? you might ask. Well, simply put, starting a SIBO protocol can be cumbersome and difficult. Sometimes, to ensure success, we don’t want to throw the whole kitchen sink at you—it can be more beneficial to wait and do one thing at a time.)

A gut healing protocol can look differently for everyone depending on your individual case, but it generally includes a few things. First, we work on reducing the inflammation of your gut lining with herbs and dietary changes. Then, we introduce nutrients and amino acids that support regeneration and healing of the tissue and the nerves that power the gut lining. Once these foundational things are squared away, your gut tissue will be less permeable (a.k.a. less ‘leaky’), the nerves healed, and your gut-brain will be happy again.

During the gut healing portion of your SIBO treatment, you go back to eating a whole-foods, nutrient-dense diet that is promoting of good health and digestion. No more SIBO Specific, low FODMAP, SCD meal plan.

Some Pro Tips For SIBO Treatment

It may take some time. Not every case is an open and closed book. There are many times that we feel confident it will take 2 to 3 months to eradicate SIBO, but after that duration, we still have some lingering symptoms. At that point, we’ll sit back down with you to determine if we need to change up your herbs to break your plateau, or if we should retest and find out if the lingering symptoms are due to SIBO or not.

It’s going to take some support. We’re not just talking about getting your family on board—SIBO treatment is a bumpy ride overall. it’s going to be a bumpy ride overall. During treatment, you’ll have days where you feel great, and then days you feel back at square 1. With all the frustration, Googling, and dietary restrictions, it can be easy to just give up or cut corners. SIBO patients make perfect members in our practice because when you’re feeling frustrated with the process, you can lean on your doctor to help you with guidance. And when you’re sick of the same old meals, you can lean on your dietitian as an added resource.

SIBO treatment doesn’t have to be all-consuming and completely overwhelming. When you have the right steps in place, and the support of doctors and dietitians who want to see you get well again, you can beat SIBO—and help keep it from coming back again.

Interested in learning more about SIBO? Go back and read our overview of SIBO, and stay tuned for how we recommend keeping your sanity while on the SIBO Specific diet.

Dr. Cassie Wilder

Dr. Cassie Wilder is a registered Naturopathic Medical Doctor (NMD) and founder of MIMC. Her passion is empowering her patients through education, understanding, and support through their healing journey. After graduating from Iowa State University with a Bachelors of Science in Kinesiology and Health, Dr. Wilder earned her Doctorate of Naturopathic Medicine from Southwest College of Naturopathic Medicine & Health Sciences, a fully accredited and nationally recognized institution in Phoenix, AZ. During her clinical training, she received extensive hands-on training with many leading experts in the field of functional medicine and developed a passion for treating hormonal imbalances, thyroid disorders, cardiovascular concerns, and adrenal fatigue.