The Best SIBO Treatments, Herbal Supplements and Natural Remedies

by health and nutrition advice journalist

This post is the second in a three-part series on Small Intestine Bacterial Overgrowth focusing on SIBO natural treatments, antibiotics, herbal supplements and lifestyle changes. You can see Part 3 on SIBO diet, on-going healing and recovery here. And brush up on see Part 3 on SIBO symptoms and testing here.

When I finished my SIBO treatment last month, I was convinced I still had critters.

Even though I had been taking herbal antibiotics for nearly 6 weeks, my system still felt off. My stomach continued to bulge, my digestion was pokey. I was burping during meals, no matter how many FODMAP’s were on my plate. And despite these symptoms (which I laid out in Part 1 of this series) having gotten a little better, their persistence seemed to be evidence that whatever hodgepodge approach I had taken to ridding my small intestine of its bacterial burden, had failed.

This SIBO-style paranoia seems to be common among sufferers I’ve spoken to. And for good reason. The first being that treatment options are complicated, varied, and often take doctors a few tries to tailor to the individual. The second being that even if one works the first time, SIBO is a chronic condition that often relapses within 3 weeks of finishing treatment.

In case that thoroughly bummed you out, I’ll share with you the little piece of news that I received this week that put a pin in my SIBO stress balloon (and, the one slowly deflating in my abdomen): after two months in the weeds, I’m officially SIBO free!

I’ve included a screenshot below of my two tests side by side in case you’re curious. If you’re wondering how to read them or how it works, make sure to brush up on SIBO 101 in this post.

As I waited for the results, which came 3 weeks after I finished my course of herbal antibiotics (the Biotics protocol discussed below), I planned for the worst and continued to diligently research other treatment options, debate which route I would try for the next round, and question whether I would ever end up desperate enough to get my meals in the form of a medical liquid (i.e. the elemental diet).

Today’s post is a result of that deep dive. In it I lay out the three main phases of SIBO treatment, the three primary approaches to killing your bacteria, and the many many herbal supplements and lifestyle changes that are recommended to treat symptoms and aid in the process.

One prong of the treatment plan that’s not discussed as often is optimism. I can’t stress enough how bad stress is for any chronic condition, even though chronic health conditions are some of the most stressful life forces on the planet.

As hard as it may seem, try to stay positive.

My guiding light throughout this process was knowing that my experience with SIBO could help others navigate it down the line. And you don’t have to be a blogger with a platform to embrace that silver lining. I got some wonderful emails from friends who took meticulous notes (and created fabulous spreadsheets) during their year-long battles with SIBO.

Remember that dealing with SIBO is a wellness project in and of itself. Embrace the trial and error. And even if the road feels long, once you take the scenic route up Health Mountain, you’ll be that much better equipped to guide others on the journeys that lie ahead.

With health and hedonism,

p.s. If you’re looking to save time in your low FODMAP kitchen, check out some of these fabulous store bought sauces, spice mixes and condiments.


Though doctors are becoming savvier about testing for SIBO, they often focus on just the kill phase and don’t always appreciate the full breadth of what it takes to eradicate it for good.

Here is how I break down the timeline:

1. The Kill Phase (2 – 6 weeks)

This phase lasts as long as the medication protocol prescribed, most commonly a generic antibiotic like Rifaximin or one of the herbal protocols. There’s a debate as to whether a low FODMAP diet is beneficial during the kill phase, which I will discuss briefly at the end of this post. For those with severe symptoms, beginning a low FODMAP protocol will help jump start the healing phase and provide some relief, but you don’t want to be so strict that the bacteria go into hibernation because they’ve fully lost their food source.

2. The Healing Phase (2 – 3 months)

It’s recommended that you retest for SIBO exactly two weeks after the antibiotic protocol is complete. Some people who are feeling better will continue onto the next phase regardless since the test is expensive. Others will wait until a negative result is achieved, and then proceed with some diet modifications that aim to heal the intestinal lining and rebuild the immune system, usually the slow reintroduction of high FODMAP foods, coupled with the GAPS diet.

3. The Recovery Phase (On-Going)

SIBO is a chronic condition. If it comes back, it’s not an indication that the treatment plan didn’t work, but rather, that the root cause hasn’t been dealt with properly on an on-going basis. This is where a lot of the lifestyle modifications come into play, and in some cases, where it’s necessary to continue certain supplements, specifically the ones that improve motility (i.e. those that make sure you’re pooping properly).

Today’s post will mostly focus on the kill phase, though some of the lifestyle recommendations pertain to phase 2 and 3, which will be discussed in the last part of this series.


The options for treating SIBO during the Kill Phase fall into three categories: regular antibiotics, herbal antibiotics, and The Elemental Diet. With the exception of the latter, which is full package approach, there are still plenty of dietary and lifestyle changes, and additional supplements, that will help the medication do its job. I’ll get to those later. For now, let’s talk about the pro’s and con’s of natural treatments versus the pharma route.

The first thing that your physician should keep in mind is that the treatment for SIBO is different depending on whether it is methane or hydrogen producing, and presenting symptoms as constipation (SIBO-C) or diarrhea (SIBO-D). There is usually a strong correlation with these symptoms and which gas is present (methane-C, hydrogen-D), but not always. Make sure to discuss both with your doctor to ensure you choose the right protocol.

1. Antibiotics (2 weeks)

There are several pharmaceutical antibiotics which are commonly prescribed for SIBO: Neomycin (better for Methane dominant), Metronidazole, and Rifaximin. The benefits of antibiotics top out after 3 weeks, so a 2 week course is the sweet spot.

Rifaximin (generic: Xifaxan) has the best reputation of the group, even among naturopaths, as it’s an antibiotic with “eubiotic effects.” It specifically targets the area we need to eradicate—only killing bacteria in small intestine. According to studies, the side effects are mild and the die-off of beneficial species of bacteria in the colon is minimal. For those who are wary of antibiotics, this isn’t a bad one.

However, the main problem with Rifaximin (and all other pharma options in this category) is that with repeat use, you increase the likelihood of becoming resistant. Meaning, it might be worth one try, but you don’t want to get into a cycle of use, especially when there are other natural options that have been proven equally effective with fewer long-term risks.

2. Herbal Antibiotics (4 – 6 weeks)

People don’t necessarily gravitate towards herbal options just because they’re more “natural.” Rather, certain combinations of herbal antibiotics have been proven in studies to be just as effective, if not more effective than their pharma counterparts.

The downside: more pills, for longer, with the possibility of GI side effects. Just because herbs are natural doesn’t mean they’ll be tolerated by everyone. I certainly experienced discomfort and an increase in my constipation symptoms while on the Biotics formula.

The upside? You can purchase these herbs without a prescription and experiment on your own. Which, considering you can now take a SIBO test at home, is an affordable option for those who aren’t able to invest in the helping hand of an integrative doctor.

So what are the best protocols for herbal antibiotics? The two most commonly used herbal blends in Dr. Alison Siebecker’s practice, who is commonly thought of as the pioneer of SIBO, are:

Typical dosing is: 2 caps, twice a day, for 4 weeks. For what it’s worth, I did the Biotics system for 6 weeks.

The two protocols above combine several individual herbs that are thought to be helpful, including berberine herbs, ginger and oregano. There’s definitely a big pro to having a formula already sussed out for you. But another route is to design your own treatment using a combination of the below herbs. Dr. Allison Siebecker recommends 1-3 in combination, for 4 weeks, at highest dose suggested on product labels.

3. The Elemental Diet (2 weeks)

If all else fails, there’s always the elemental diet. It is thought of as a last resort because of the extreme unfun-ness of the protocol, which involves drinking a medical solution for all meals for a 14 day period. I can’t imagine ever doing this, but it’s a relatively quick strategy that’s proven 85 percent effective at starving out the bacteria, while, on a purely elemental level, feeding the person.

The mixture includes liquid nutrients in an easily assimilated form that is used in hospitals on GI patients whose system needs to heal. The nutrients get absorbed quickly and easily in the first leg of the digestive labyrinth, meaning they never make it to the area of the small intestines where unwanted bacteria congregates in SIBO patients.

The protocol is suggested for 14 days, with a retest taking place on the 15th day. Overnight results should be requested so that you can immediately start the diet for an additional week if there’s still a positive.

Again, this is if all other protocols fail. It’s not recommended to take antibiotics or herbs during the elemental diet because the bacteria, without food sources, will essentially be hibernating or die off on their own, as intended by the diet.

Get more SIBO info right in your ear…


Since antibiotics and herbal alternatives can be used interchangeably as killing mechanisms, what really gives you an extra edge is how you support your treatment through lifestyle changes and supplements that treat the root cause of your SIBO.

As you may remember from lesson 1, one of the biggest underlying problems that contributes to SIBO is a screwy, slowed Migrating Motor Complex (MMC). Luckily, there are several easy changes you can make to your diet to help your digestive system catch up. We will talk about these more in the next installment.

For now, some quick tips:

Sometimes the MMC can’t be stimulated properly through diet alone, which is where prescription medication and additional supplements come in. This list may seem overwhelming, so remember that this is not an “all of the above” suggestion. Rather, some of these supplements can be used as added strategies down the line or to treat discomfort throughout the process as needed.


Most people who talk about SIBO treatments take the starve and kill strategy: switch to a diet that’s low in foods your bacteria like to eat (fermentable carbohydrates) to try to reduce them, and add in a medication that will further the extermination. Usually this involves a combination of the low FODMAP Diet and the Specific Carb Diet, and also means eliminating fermented, probiotic foods, and inulin-rich prebiotic foods that have long been touted as a healthy gut’s best friend.

There is another school of thought, however.

And that is to use probiotic and prebiotic supplements as a means of righting your overall bacterial imbalance.

The research is much more sparse for this line of treatment, but there have been several small studies that indicate using probiotics doesn’t hurt, and its ability to help is strain specific.

The argument for probiotics, as Dr Jason Hawrelak explained in his lecture on the subject, is that they can speed transit time, stimulate the MMC, help heal leaky gut by regrowing villi, and ease gut hypersensitivity which is common with SIBO.

I don’t bring this up to confuse you, though of course offering up a mode of treatment that is in direct conflict with the ones I just mentioned above, does seem downright confusing! The point is that every body is different. There are many solutions and ways to tackle the problem of SIBO, and there’s not a single approach yet that has been proven to be “right.”

If adding rather than taking away seems like a better approach, you can do more research on probiotics and SIBO, and/or experiment with prebiotics like Allicin, Partially Hydrolyzed Guar Gum, and GOS’s.

As Dr Jason Hawrelak argues, SIBO sufferers react to high FODMAP foods because there’s something wrong with their gut not because the FODMAPs are harmful. And using probiotics to shift the bacterial ecosystem usually means an overall smaller population of bacteria in the small intestine.

The low FODMAP and SCD diets target carbs because that’s what bacteria like. They are also a great tool for reducing symptoms and giving patients a sense of control. But the ultimate outcome you want is to be able to eat all the beneficial vegetables and treat the underlying cause to get you there.

And that dietary part of the debate–both what to do during treatment and afterwards to prevent relapse–is where we are going to pick up next time!

Do you have questions about SIBO and how to treat it with diet?

Need 4-weeks worth of easy low FODMAP recipes with a step-by-step meal plan laid out for you?

I recently added a low FODMAP track to my online course, 4 Weeks to Wellness. You’ll now receive a 20 recipe cookbook, shopping lists, elimination diet guidance and reintroduction worksheets, in addition to the many other resources in the normal program.

This content was originally published here.

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