Dr Pimentel SIBO IBS Drugs

SIBO Expert Dr. Pimentel on Drugs for SIBO and IBS

In my last post, I recapped Cedars-Sinai SIBO expert Dr. Mark Pimentel’s Twitter chat on food and diet related questions on IBS and SIBO. Now, I’ll recap his answers to questions about drugs for SIBO and IBS and explain to  you what’s new and surprising in the world of SIBO and IBS drugs.

Drugs for IBS generally attempt to just treat the symptoms without solving the root cause. Doctors or patients often use Imodium or Pepto Bismol, or prescription drugs like tricyclic antidepressants, to treat IBS-D by slowing down the digestive system. For IBS-C, patients and doctors use drugs that cause more water to enter the digestive tract, like magnesium, or use laxatives, which irritate the digestive system.

For SIBO, treatment with drugs usually consists of antibiotics (pharmaceutic or herbal) followed by a prokinetic to stimulate the migrating motor complex’s cleansing waves. This protocol is what I followed when treating my SIBO.

Let’s see what Dr. Pimentel had to say about drugs for SIBO and IBS in the Cedars IBS Chat on Twitter last month.

You need antibiotics to fully treat SIBO.

Often times I see people say that a low FODMAP diet is all you need to treat SIBO. While a low FODMAP diet helps alleviate many SIBO symptoms, it won’t treat the underlying problem. This tweet addresses a similar issue: can you just take laxatives and treat the symptoms of SIBO? Will this be enough to cure it?

The answer, as I suspected, is no. It’s interesting to me that laxatives actually do help reduce methane. Presumably this is because getting things moving through your gut instead of letting fermenting in your digestive tract reduces the food for the bacteria. Less food for bacteria = less bacteria.

Dr. Pimentel then states what I suspected: that you really do need to get rid of all the bacteria with antibiotics instead of just reducing them through laxatives. I suspect this same reason is why it doesn’t’ work to do a low FODMAP diet without using antibiotics first. The diet helps by giving the bacteria less food, but ultimately, we need a stronger method to get rid of the bacteria first. That’s what the antibiotics are for.

Speaking of Antibiotics and the Low FODMAP diet, do not combine the two!

This tweet has since been removed but from the response it seems that it asked why a course of antibiotics might not work. It seems pretty common in SIBO treatment that a course of antibiotics fails. Many people have to take multiple antibiotic courses to eradicate their SIBO. For others, it doesn’t seem to work at all.

Often on the SIBO groups I’m a part of, I see people asking whether they should start a low FODMAP diet while on antibiotics. The answer, as always, is NO!

As Dr. Pimentel notes, the bacteria go into survival mode when they do not have enough food. This makes them harder to kill. Instead, you need to feed them with lots of nice yummy FODMAP containing foods. When the bacteria are well fed and replicating is when the antibiotic is most effective.

So remember…if you’re on an antibiotic (at least a pharmaceutical one) then wait until after you’re done to start your low FODMAP diet.

It’s unclear what drugs treat Hydrogen Sulfide, a new SIBO gas.

Hydrogen sulfide in SIBO is not something I knew about until very recently. A standard breath test for SIBO tests for methane or hydrogen. However, sometimes people will have negative breath tests and still have symptoms.

A 2016 study showed that the culprit in those cases might be a gas called hydrogen sulfide. Like methane and hydrogen, bacteria that overpopulate the intestine in SIBO can give off hydrogen sulfide. But there is no widely available, standard breath test yet for hydrogen sulfide.

Unfortunately, it seems like even the expert, Dr. Pimentel, doesn’t have a good answer yet for how to treat hydrogen sulfide. That’s disappointing, but hopefully something that researchers are studying. It would be useful to have more antibiotics or other drugs for SIBO and IBS that attack a wider range of bacteria and symptoms. Perhaps studying hydrogen sulfide will lead to that.

In the meantime, the takeaway is that if you have a negative breath test but still have symptoms, you may have SIBO with hydrogen sulfide producing bacteria. One potential treatment idea would be to try an Elemental Diet. That way, you don’t have to wonder if you have the “right” antibiotic to kill the bacteria because you are starving all of them, presumably.

Rifaximin doesn’t cause bacterial resistance.

You know how I mentioned earlier that it’s very common to need multiple courses of antibiotics? Back to that theme.

Antibiotic resistance happens when bacteria adapt and change after encountering an antibiotic. They change so the next time you take the antibiotic, the bacteria can resist it and continue thriving. Sadly for us this means the antibiotics stop working.

Many times I’ve heard from SIBO patients who say their doctor treated them with Flagyl, Cipro, or some other antibiotic that is not Rifaximin. I’m skeptical of the success of those because Rifaximin is specifically absorbed in the small intestine, unlike other antibiotics. That Rifaximin doesn’t cause antibiotic resistance confirms another good reason to use it as a first line treatment for SIBO.

Bottom line: if your doctor prescribes you an antibiotic other than Rifaximin as the first attempt at SIBO treatment, ask him/her why. Insurances often require prior authorization for Rifaximin, so be prepared to tell your doctor why Rifaximin is superior if he/she does not already know. Not all drugs for SIBO and IBS are created equal!

What the heck is the diarrhea drug Ondansetron?

I will say it’s pretty rare when there are drugs for SIBO and IBS that I haven’t heard of. This is one such case though!

IBS and SIBO often manifest in diarrhea (mine included!). I thought I heard of pretty much all the drugs used to cope with diarrhea. That includes tricyclic antidepressants, antispasmodics, imodium (which is an opiate). But I hadn’t heard of this drug that Dr. Pimentel mentions, called Ondansetron. The brand name is Zofran.

Doctors generally prescribe Ondansetron to alleviate vomiting and nausea caused by chemotherapy. Chemotherapy drugs cause the body to release serotonin cells in the small intestine, which stimulate the vomiting reflex. By blocking this serotonin, Ondansetron prevents vomiting. Instead of swallowing the drug, it’s dissolved on the tongue.

Studies have shown that Ondansetron can improve diarrhea for IBS patients. Personally, I wish my doctors had known about this drug back when I went literally years with just an IBS diagnosis. I found that tricyclic antidepressants didn’t change my symptoms, and imodium caused bloating and discomfort.

Have you tried Ondansetron for IBS? What was your experience? Let me know in the comments!

Magnesium: A-ok to take, but beware…

Magnesium can be a great supplement. It keeps the heart, bones, and teeth strong. It can help relieve stress and relax muscles. Unfortunately, it also draws water into the intestines which can cause diarrhea.

I once saw a naturopath who diagnosed me with a magnesium deficiency by testing my muscle reflexes. He prescribed me a magnesium supplement…which I definitely did not take because I wasn’t about to chance more diarrhea! But sometimes, we really do need more magnesium than we are getting through our diets.

I think the original questioner here wondered whether taking a prokinetic, which stimulates the migrating motor complex, would work at cross-purposes with taking magnesium. But prokinetics and magnesium work differently. Magnesium draws water into the intestines, which causes looser stools. A prokinetic causes more cleansing waves of the small intestine.

So magnesium and prokinetics don’t work the same way. As Dr. Pimentel says, one should not affect the other. Just make sure that when you take magnesium, you start with a low dose and work your way up to make sure you won’t wind up in the bathroom too much! That goes for whether you take it with a prokinetic or by itself.

That’s all for now on drugs for SIBO and IBS…

Well, I think that covered all the questions Dr. Pimentel answered about drugs for SIBO and IBS. Were there any questions I missed, or anything you’re wondering about? Don’t forget to check out my post about what Dr. Pimentel had to say on food and diet, and leave me a note in the comments below!


  1. Rifaximin is neither affordable nor permited for treating IBS and/or SIBO in Australia. I’de like to use Erythromycin at a dose of 250mg bid, 7-10 days. Clearance and prokinetic in one. I would appreciate Dr Pimentels’ response indicating clinical advantage/disadvantage if possible please.

  2. Hi Margaret, low dose erythromycin is used solely as a prokinetic, at very low doses (I cut a pill into quarters that each end up being around 62mg I believe). At that low dose, I’ve been told, it doesn’t act as an antibiotic because it’s so small–only acts as a prokinetic at that dose. I have never heard of Erythromycin being used short term in larger doses as an antibiotic for clearing the bacteria in SIBO, so I don’t believe it’s used for that, probably because it isn’t effective at that. If you can’t get Rifaximin, I might suggest looking into herbal antibiotics, some of which have also been studied for SIBO and found as effective as Rifaximin. You can read more about those here: https://sibosense.blog/2018/06/17/all-about-treating-sibo-with-herbal-antibiotics/

    Best of luck!

  3. To me, my worst symptom is terrible breath from SIBO. I don’t see many people speak about that problem. I’ve been on two courses of antibiotic so far. Is this a common symptom.

    1. Hmm, I haven’t really heard that as a common symptom. Maybe ask your doctor? Sorry, I don’t have any advice about this one!

  4. All Dr.pimentel is talking about here is DIAREA!!! I wish I had diarea !!!!–I have IBS CONSTIPATION !!!–he says only that it is harder to treat ..so why nobody is adressing us IBS-C sufferers ? wwe are in pain and need too and even more so !!!!btw–Neomicyn (mentioned many times together with Rifaximin for IBS-C ) is OTOTOXIC !!!=toxic for the inner ear !!! it can cause hearring loss–I am a proffetional musician–so for me it is absolutly no option

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