SIBO Antibiotics

sibo antibiotics xifaxan

SIBO antibiotics are often one of the first recommendations by any gastroenterologist for SIBO treatment. This is because antibiotics can be one of the quickest and most effective treatment options available for people suffering from SIBO or IBS. But, there are things you need to know before proceeding with one of these treatment options. Personally, I have experience using Xifaxan for SIBO and it was very helpful for me, but there are things I wish I knew before using this antibiotic to help my gut.

In this article, we will break down everything you need to know about SIBO antibiotics including how they work to treat SIBO and IBS, which antibiotics are used, what Xifaxan is, what it means if they don’t work, and what you need to know about these treatment protocols before proceeding for the best outcome.

How Do Antibiotics Treat SIBO and IBS?

First of all, if you don’t understand the basics of small intestine bacterial overgrowth which is found in 60-80% of people with IBS, I would recommend reading this article.  

Basically, antibiotics work to treat SIBO by killing bacteria in the small bowel. Antibiotics do this by either stopping bacteria from replicating or destroying them. The reason we want to kill bacteria is because people who have SIBO have accumulated too much bacteria in their small intestine (where there should be smaller amounts) which causes a plethora of debilitating digestive symptoms such as gas, bloating, diarrhea, constipation, fatigue, and altered stool formation. When you treat this bacterial dysbiosis in the small intestine with specific antibiotics and reduce the amount of gas being produced it can get rid of symptoms.

Sometimes just treating this bacterial overgrowth can solve the problem for some people but in others, they will need to address other underlying causes which enabled this overgrowth in the first place. I will touch upon prevention later on.

Xifaxan for SIBO and IBS

Xifixan for IBS

There are a few different antibiotics which are usually prescribed to treat SIBO and IBS but the main antibiotic used is called Xifaxan (Rifaximin). Xifaxan is a non-systemically absorbed rifamycin with antimicrobial activity against gram-positive and gram-negative aerobic and anaerobic organisms.1 Xifaxan is used to treat travelers diarrhea, hepatic encephalopathy, IBS/SIBO, and a few other bowel infections.2

The main differentiator between Xifaxan and other antibiotics is that it has very minimal absorption and works specifically in the gastrointestinal tract. This means that there is minimal risk of toxicity or systemic side effects like you can get in other systemic antibiotics. Also, the solubility of the drug increases 100-fold in the presence of bile acids (which are produced in the small intestine) which means that its antimicrobial effect is achieved mainly in the small bowel and less in the colon.3 On top of that, Xifaxan has shown to decrease mucosal inflammation which is hypothesized as another reason it helps IBS patients. Because of these properties, Xifaxan is a top antibiotic chosen for SIBO treatment.

Xifaxan for IBS-D

Xifaxan has been studied and used in all subsets of IBS and SIBO patients including diarrhea, constipation, and mixed type patients. But, it’s important to understand that there have been differences in study results using Xifaxan and usually different protocols are administered between diarrhea and constipation type patients. In this section we will go over Xifaxan’s use in IBS and SIBO patients with diarrhea.

Xifaxan is normally one of the best antibiotics to be used with SIBO and IBS with diarrhea. In a number of different studies it has been shown that a 2 week course of Xifaxan at a dose of 550 mg 3 times per day provides significant relief of IBS/SIBO symptoms, bloating, abdominal pain, and loose or watery stools.

The only thing you need to keep in mind when using antibiotics is that you can relapse after treatment which is why it’s important to take preventative measures and continue to work on your overall digestive function. That being said, using Xifaxan for people with diarrhea as a predominant symptom is usually a very effective option.

Xifaxan Dosages for Diarrhea

  • 1200 mg per day for 10 days with 5 g per day of partially hydrolyzed guar gum (source)
  • 1200 mg per day for 14 days (source)  

Xifaxan for IBS and SIBO with Constipation

Xifaxan is also used in constipation cases but there has been different research findings and outcomes using it with constipation. It’s important to note that using Xifaxan alone is usually only used in people with diarrhea or mixed type symptoms and not as often in constipation cases. But, there has also been a small amount of evidence that Xifaxan alone can help some people with constipation, like this study.

Like any medical treatment each person has a unique body and using Xifaxan alone for constipation may be helpful or it may not. But, it has also been reported that using just Xifaxan alone for treating SIBO with methane dominant archaea is usually not as effective as using Xifaxan in combination with Neomycin.

In this study, they took patients who tested positive for methane on the SIBO breath test and split them up into 3 groups. They gave one group just Rifaximin, one just Neomycin, and another group a combination of Rifaximin and Neomycin. They then followed up after treatment. The results showed that 87% of the Rifaximin and Neomycin group eradicated the methane on their breath test compared to 33% of the patients in the Neomycin group and 28% of the patients in the Rifaximin group. Wow, that’s a big difference.

This shows why Xifaxan alone is usually only prescribed for patients with diarrhea type symptoms. The reason this is the case is because different antimicrobials work on different organisms in the gut.

Xifaxan Combo Dosages for Constipation

  • 1200 mg Rifaximin + 1000 mg Neomycin per day for 10 days (source)

The Pros and Cons of Using Xifaxan for SIBO

sibo antibiotics pros and cons

There are pros and cons when deciding to use SIBO antibiotics like Xifaxan. Here is a list of both sides of the equation so you can make the best decision possible.


  • Works quickly when it is effective
  • Protocols have been researched thoroughly
  • One of the strongest treatment options
  • Xifaxan is a non-absorbable antibiotic so it doesn’t cause as many systemic side effects
  • Xifaxan can reduce mucosal inflammation


  • Xifaxan is very expensive, without insurance it usually costs around $1,500
  • Xifaxan can still cause bad side effects even though it doesn’t happen as often since it acts mostly in the gut
  • You can still relapse after a successful treatment since it doesn’t address the underlying cause in a lot of cases
  • Xifaxan isn’t as effective in constipation or hydrogen sulfide cases and needs to be combined with other antimicrobials

My Experience Using Xifaxan for SIBO

As a chronic SIBO patient who has gotten a lot better over time, I have experience using Xifaxan for SIBO treatment. Personally, it was very effective for me but I did relapse after a few months. In the past I used to have more diarrhea type symptoms and doing a treatment with Xifaxan cleared that up right away. I haven’t had urgent diarrhea type symptoms since which is positive. But, it wasn’t until I addressed my bowel issues with a holistic treatment approach using herbs, tea, diet, and motility agents that I found consistent improvement.

From my experience, if you are a diarrhea type SIBO or IBS patient Xifaxan can be a very effective antibiotic to help you. If you struggle more with constipation symptoms, you obviously would want to try the Xifaxan and Neomycin combo or use herbal antibiotics. But, you need to remember that finding consistent improvement in your bowel symptoms takes a holistic approach. You will need to work on eating a healthier diet, promoting motility in your gut, addressing other issues that helped cause the bacterial overgrowth, and developing a comprehensive strategy. For a lot of people (myself included), it takes a few different treatments and other natural changes to find lasting relief.

In summary, antibiotics can be a very helpful treatment option but it will not be a magic cure for most people. I personally think it’s smart to stay as natural as possible at the beginning until you find that you need pharmaceutical drugs.

Relapse Rates After SIBO Antibiotic Therapy

sibo antibiotic relapse rates

I think it’s important to touch upon relapse rates after using antibiotics because this can help influence your decision whether to try natural treatments first or go straight for antibiotics, especially if you have to do multiple courses. I think you will find that in the long run, it’s important to incorporate mostly a natural protocol while using pharmaceuticals only when your symptoms are very severe.

In this study, the aim was to investigate SIBO recurrence in patients after a successful antibiotic treatment. They took 80 patients and reassessed them after 3, 6, and 9 months after normalization of their breath test. The results were very informative and important for people to understand who are using antibiotics.

The Results:

  • 3 months after successful antibiotic treatment 10 patients (10/80 or 12.6%) tested positive for SIBO again indicating relapse
  • 6 months after successful antibiotic treatment 22 patients (22/80 or 27.5%) tested positive for SIBO
  • 9 months after successful antibiotic treatment 35 patients (35/80 or 43.7%) tested positive for SIBO

They also showed that older age, a history of appendectomy, and chronic use of PPI’s were associated with positive recurrence. This means that if you have other health issues which are causing issues with your gut function you will be more likely to relapse and be a chronic patient.

Basically, this study is very important to understand. It shows that antibiotics can definitely help a lot, but they most likely will not be a magic cure. They are only one piece of the healing puzzle. A lot of people deal with relapse and have to find other strategies to help maintain and prevent recurrence of their symptoms.

Why Does SIBO Relapse Occur?

This is the magic question for any doctor, patient, or researcher dealing with SIBO or IBS. Whoever figures out a solution to the relapse problem will be a rockstar. Often times this condition can be chronic and like the study above showed, recurrence can occur after a successful course of antibiotics.

The main reason recurrence occurs is thought to be because of an issue with the function of the gut. Some patients who develop bacterial overgrowth also have damaged cleansing waves in their small intestine which means that they do not clear bacteria and undigested materials as powerfully as other people. When these cleansing waves are damaged in the small intestine it allows bacteria to accumulate where they shouldn’t be and cause symptoms. Some of the main prevention strategies which help SIBO patients are:

  • Healthy lower carbohydrate diet
  • Prokinetic agents (natural or pharmaceutical)
  • Fixing other issues in the body causing decreased motility
  • Reducing stress and making healthy life changes (high stress can decrease motility)

What Does it Mean if SIBO Antibiotics Don’t Work?

For some people, antibiotics can be very effective. For others, for some reason or another, they may not work or they may only work for a very short period of time. This can be super frustrating. So what does this mean?

This can mean a few things:

  • The SIBO antibiotic protocol was not correctly selected for your specific gut bacteria
  • You may need additional courses or an elemental diet to treat your stubborn microbes
  • Your gut does not respond to the antibiotics because of antibiotic resistance
  • Your problem isn’t SIBO and instead may be a different type of gut dysbiosis or health issue  
  • If you relapse super quickly, you may need to focus on addressing other issues

Can You Treat SIBO Without Antibiotics?

yes, you can treat sibo without antibiotics

This is another question many people ask after looking at SIBO antibiotic relapse rates, side effects, and the cost of purchasing Xifaxan. Yes, you can definitely treat SIBO without antibiotics and in a lot of cases, this can be a better strategy over the long term.

When you realize that most people will relapse after a successful course of antibiotics it makes sense to consider treating SIBO naturally and taking a more gradual approach. Honestly, from my experience dealing with SIBO, I would recommend trying natural treatments first.

There are a few treatment options which have been proven to be effective:  

Concluding Thoughts on SIBO Antibiotics

If you’re thinking about taking SIBO antibiotics like Xifaxan they have definitely been shown to work effectively and quickly. The only issue is the cost, side effects, and relapse rates when using antibiotics.

From my experience, if you are someone who is dealing with a stubborn case of SIBO, and willing to spend a lot of money on Xifaxan it can be a good option. On the other hand, if you don’t want to spend as much money and want to take a more gentle long term approach, using a natural treatment option is going to be your best bet. Using herbal antibiotics, the elemental diet, or long term diet changes can be just as effective!