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“My Breath Smells Like Poop!”

Usually by the time someone comes to us at WholeHealth Chicago with this complaint, they’ve already taken the obvious route. Ralph, a healthy looking guy in his 30s and recently married despite his halitosis, had already seen:

–His primary care physician, who wasn’t sure he noticed anything odd about Ralph’s breath at all, but suggested regular brushing, flossing, and tongue scraping.

–His dentist, who did a careful deep cleaning and then when Ralph showed no improvement referred him to an ear-nose-throat (ENT) specialist.

–The ENT guy did a nasal endoscopy and told him his sinuses were fine, but suggested a gastroenterologist.

–The GI specialist performed a gastroscopy, thought there might be a little acid reflux, and prescribed a proton pump inhibitor (like Nexium), which did nothing.

Ralph’s morning oral hygiene ritual, as you might have guessed, was quite involved. He’d awaken anxiously hoping his new wife wasn’t yet awake so he could do a thorough mouth cleaning and return to bed with fresh breath.

“My breath smells like poop!” Ralph told me when he came in. This was no new problem for him. He’d been alerted to his halitosis by his mother, his grammar school and high school friends, his frat brothers (who gave him just the nickname you’d expect from frat brothers), and some of his longer-term match.com meet ups.

He went through life armed to the teeth (literally) with breath-betterment products.

Could it be SIBO?
Ralph had seen information about small intestine bacterial overgrowth (SIBO) online. Had he read the Health Tip I wrote several years ago I’m guessing he would have recognized himself immediately. I was really surprised how similar Ralph’s case was to that one. However, as you’ll see, Ralph’s case was also unusual. Parallel story, different ending.

You, of course, as a devoted student of Dr. Google, are aware that your large intestine is filled with five pounds of bacteria containing about 1000 identified species, many of which produce methane, which is why farts smell like farts.

For some people, bacteria meander to the small intestine and set up house. The main symptom of SIBO is bloating, with some affected people reporting they can literally see their stomach expand after eating.

In addition, movement through your intestines isn’t just mouth-to-anus. In one of many sickening moments of medical school, in physiology class I learned of an experiment performed in the 1930s in which a purple dye was administered by enema to healthy volunteers (likely medical students) and traces of the dye were found in their mouths the next morning.

“Now you understand morning breath,” chortled the professor as 200 students groaned aloud.

I had to share that with you.

Ralph takes a breath test
Anyway, back to Ralph. I ordered a take-home breath test by Genova Labs. You start by drinking a small amount of lactulose, which encourages bacteria to produce gas. Then, every 30 minutes for two hours, you blow into a balloon-like device, snap on a glass vacuum tube to collect the air, and FedEx what look like four empty tubes to the lab for analysis.

Most patients with SIBO have excessive amounts of methane, hydrogen, or both. The test results showed Ralph’s was predominantly methane and the conventional treatment–ten days of an insanely overpriced antibiotic called Xifaxan–usually works nicely (generally insurance pays for it, but at $60 a tablet, they’re not enthusiastic).

Remember, Ralph’s main symptom is his breath. He really didn’t have any symptoms of SIBO, just a positive breath test that was picking up the methane in his mouth.

Ralph reacted oddly to Xifaxan. He reported his poop-smelling breath disappeared for two weeks after completing the meds, but then it quickly returned. I recommended that we next try three weeks of products favored by naturopathic physicians: CandiBactin A/R and CandiBactin B/R, both by Metagenics. The outcome was the same. Ralph experienced about a month of relief before reverting to his stinky breath.

A second line of conventional treatment is a pair of antibiotics, Neomycin and metronidazole (Flagyl). Because Neomycin can affect hearing, you can only use it only for a few days. Metronidazole is widely used for a variety of infectious conditions, including traveler’s diarrhea, intestinal parasites, and bacterial vaginosis. It’s even applied to the skin for rosacea.

A lightbulb moment
But then a lightbulb went on in Ralph’s brain. He remembered that some years earlier when he was prescribed metronidazole for traveler’s diarrhea, his breath had been fine. He had even renewed that prescription just to get a few more weeks of relief.

Could he just stay on metronidazole forever? Reading aloud to Ralph the drug’s long-term side effects discouraged us both. But then I came across this interesting article from the Iran Journal of Pediatrics in which doctors faced the same fart-breath challenges in kids. They had a compounding pharmacy make metronidazole into a mouthwash, which the kid would swish around every morning and spit out. Success rate? An astonishing 97%.

Obviously, I ordered a bottle of the stuff for Ralph from the compounding pharmacy we use. The pharmacist had heard of it and said it was easy to make and not very expensive.

So, you might ask, where is the odor coming from? Here are some drawings of tongues for you to enjoy with your croissant.  Look at the different bud-like structures, called papillae. It’s been discovered (so I read in the Iranian article) that certain species of bacteria get deeply embedded into the papillae, well beyond the reach of toothbrushes, scrapers, and standard mouthwashes.

These were bacteria I had never heard of: Solobacterium moorei and Eubacterium sulci, which are far more prevalent in halitosis sufferers than in the general population. When they thrive, these bacteria literally gush out methane.

In a tidy end to this story, I allowed Ralph a couple of weeks of metronidazole tablets while the pharmacist prepared his mouthwash, which both knew would work. And it did.

Be well,
David Edelberg, MD

Leave a Comment

  1. Margaret says:

    Does the mouthwash get rid of bacteria or so they grow back?

  2. Irma Flores says:

    Can Pre and pro biotics help with this condition??

  3. Sam Crawford says:

    Finally! There may be hope for me. I have suffered with horrible morning breath that smells and tastes like poop for years. You could easily insert my name where Ralph’s appears in this entire article and that would describe my journey, Including testing positive for SIBO. The only problem is I believe I suffered an allergic reaction to Flagyl 30 years ago and to this day is the only medication I tell doctors and pharmacist that I’m allergic to. Although, I believe I may be allergic to Flagyl I’m tempted to try the mouthwash to see if it works even though it may cause a negative reaction. So my question is this, is there another antibiotic that could possibly work similarly to Flagyl?

    I really hope so.

    Thank you for writing this article . This gives me hope.

    • cliffmaurer says:

      There are other antibiotic options for SIBO, as well as some supplements and herbal preparations that work great for a lot of patients. Best to find a functional medicine practitioner that can help you sort this out. If you’re in the Chicago area, we’d be happy to help!
      -Dr M

  4. Dr E says:

    Margaret: most likely clears it permanently but if not, then repeat a course of it
    Irma: ourapothecary has a probiotic toothpaste that likely helps

  5. Is the mouthwash available for sale in your pharmacy?

  6. Mary Parisoe says:

    Great sleuthing, Dr. E!

  7. D says:

    Can I buy metronidazole mouthwash online?

  8. Mary says:

    Are the Candi/Bactin A/R and B/R helpful to Candida sufferers?

  9. Great But what about everyone else Where is the Mouthwash?????

  10. Dr. E says:

    Your primary care physician can order it made up at almost any compounding pharmacy. It is not sold over the counter. We use this one

  11. Renee Keogh says:

    What if you have a 20 year battle with Candida as well?

  12. Tom says:

    Hi all. I have had bad breath since I was 8 or 9 (I am 27 now), though when pointed out it is never just ‘bad’ it is foul. I’ve lost count of how many times people have asked if I’ve farted. It is also powerful, with people seemingly able to smell it from a distance, and also smell what I’ve eaten or drank sometimes, even if I’ve brushed my teeth etc.

    My mum also has bad breath (though I dont think she realises) and has an underactive thyroid and constipation.

    These days my oral hygiene is very good and tends to keep the bad breath at bay for a little while. I seem to get the most comments about my breath after a night of drinking, or if I am ill. I tried colonic irrigation once at my breath felt a lot fresher for a couple of days afterwards.

    My dentist cannot find anything wrong with me nor a doctor who looked at my sinuses. I get bloated sometimes and very gassy but otherwise seem to be in perfect health. Surely after such a long time with the issue, and a close relative having the same issue, this has to be something wrong with my gut?

    Please can a doctor give me their thoughts and advise me on how to get this tested (I live in the UK). This article has given me fresh hope on ending this thing that has marred my life. Thank you so much.

    • Lucy says:

      Hi Tom,

      I could have written this myself! My situation is exactly the same.

      Did you try the metronidazole? If so, did it help? Have you found anything which has helped?

  13. Dr E says:

    Hi Tom
    Ask your doctor for a prescription for just one week of metronidazole 250 mg to be taken three times a day. If it works, then you can get it made into a mouthwash that you use daily and spit out

    • Tom says:

      Thank you Dr E
      Would you recommend getting my SIBO levels tested as well?

    • Tom says:

      Hi Lucy,
      As I’m in the UK I couldn’t just order the mouthwash (I think you can in the US). I talked to a practice that specialises in Sibo/gut issues and they recommended me a number of herbal supplements, which I took for about 5 weeks. My sibo symptoms definitely improved but because of lockdown I have no idea if my bad breath got better to be honest. The symptoms have since relapsed but I haven’t been very dedicated to the recommended diet and I ran out of supplements. My advice would be to do your own research on things, maybe even test a few different food types and see how your breath is, then talk to an expert.

  14. Patricia Simpson says:

    I have poop breath for many years not my teeth causing this. I can taste it coming from my stomach. Any recommendations. I have been told for years by numerous people my breath smells. I to have GERD
    Stomach medicine such as medium doesn’t help odor.

    • cliffmaurer says:

      Hi Patricia –
      This issue is definitely deserving of a telemedicine visit. Please call in and schedule a remote visit with one of our functional medicine providers. 773-296-6700.

      We’re looking forawrd to hearing from you!
      -Dr M

  15. Tija says:


    I hope this information helps someone on this forum. My son had intermittent bouts of foul breath which could not be put down to any dental or medical issue. Having done some research I found that certain food triggered these episodes – possibly due to SIBO which we haven’t tested for. I would suggest excluding following foods and checking for symptoms. Apples, pears, raw onion, raw garlic. Also we tried substituting normal bread with gluten free variety. To our astonishment, no bad breath at all! Last night we had some apple pie – this morning, the bad breath was back, although not as bad as before. I hope to eliminate other food items as we go along and I suggest that people check low FODMAP food lists. They can sometimes be a bit contradictory but if you look into it you can hopefully figure the most offending foods and easily exclude them.I really hope that this information helps someone as we would have been so grateful if any dentist or a GP ever pointed us in this direction.

    Good luck!

  16. CJ says:


    Thank you for sharing this information.
    I have also been following the other forum “breathe smells like an open sewer” for years, I have tried a few things; seen many doctors, dentist, ENT & gastro specialist but no positive result.

    How do I book a virtual consultation with yourself or another doctor? (I don’t live in the U.S)

    Many thanks

  17. Cher says:

    I have never suffered within bad breath, up until about 2 years ago. I went to the dentist with my concerns and they told me to just use a tongue scraper and mouth wash. However, the issue has gotten progressively worse. It’s now to the point where, no matter what I do the stinky (poop) breath persists. I’ve gone to the ENT, who said there was no issue and shewed me away like I was a mental patient. I sometimes brush and tonsil stones and foul smelling/tasting mucus come up. My tongue is also white no matter how much I scrape and I just feel like there is no hope for me. Do you have any suggestions for my dire situation?

    • cliffmaurer says:

      Hi Cher,
      This sounds like quite the dilemma. There are a number of ways to approach diagnosis and treatment for something like this, and it’s best to go through your history and make some decisions about how to proceed. Please give the office a call and set up a telemedicine visit with one of our functional medicine providers so we can get you feeling better soon. Our scheduling staff can be reached at 773.296.6700.
      My best,
      Dr M

  18. Sarah says:

    I’ve had an interviewer run out of an interview and say, “I cant take it.” I recently had a little girl say, “That lady smells like poop.” My doc doesn’t believe anything is wrong. I have major bloating after eating, I have cut out gluten but still find I am bloated after eating. My dentist says I have no cavities. My tongue is white ish a lot of mornings. I am at my whits end. I have had a double bubble and they found nothing. Just tired of dealing with this!

    • cliffmaurer says:

      Hi Sarah,
      Our functional medicine providers would love to be able to help you with this. Consider scheduling a telemedicine visit with any of them; we can likely set you up with an appointment in the next few weeks. You can call our scheduling staff at 773-296-6700.

      Dr M

  19. Virginia Modingoana says:

    Hello, I live in South Africa and am happy to have found this platform. I used to feel like vomiting suicide because of this problem! I can’t even keep boyfriends, I’m now years without love in my life, would you perhaps know where I can go in Pretoria to get relief? Where can I get the mouthwash? I have a mechanical valve and am on warfarin,…..

    • cliffmaurer says:

      Hi Virginia,
      We’d love to be able to try to help you with this. Consider scheduling a telemedicine visit with one of our functional medicine practitioners and they can help get to the bottom of things.

      Best wishes,
      Dr M

  20. Karen says:

    Remi have the same problem the tablets work but when I finish them it comes back teeth are all fine all the time my tongue is yellow had enough now it’s really embarrassing what can I do

    • cliffmaurer says:

      Karen, hi.
      We’d love to be able to try to help you with this. Consider scheduling a telemedicine visit with one of our functional medicine practitioners and they can help get to the bottom of things.

      Best wishes,
      Dr M

  21. Karen says:

    Am in England

  22. Jane says:

    Hi am suffering so bad too I have been to dentist , ent, gastrointestinal an they say everything is fine .i suffer constipation and have food intolerances.am from the uk do you have a number I can contact to you thank you

    • cliffmaurer says:

      Hi Jane,
      Please call our patient services staff at 001.773.296.6700. They can set up a telemedicine visit for you with one of our functional medicine providers.
      My best,
      Dr M

  23. Kyle says:

    Dr. M

    Where can i buy this Metronidazole mouthwash? Im from Philippines. I been having this problem for more or less than 10 years. This is a life changing situation and it really bothers me a lot. Hope you could help me out. Thanks

    • cliffmaurer says:

      Hi Kyle,
      In the US, this will need to be prescribed by a physician. If you’re in the Philippines, I’m not certain if you need a prescription or not – best to discuss with a pharmacist.

  24. Rosa says:

    Hi, I’m from the Philippines & it really saddened me everyday that my breath smells like poop and I’m suffering this for almost a year. By the way, I was a positive hepatitis B. Does this disease made my breath smell like poop? To be honest, I noticed that I have a bleeding gums, white tongue & dry mouth. What to do on this? Thanks a lot!

    • cliffmaurer says:

      This definitely sounds like a dental issue, at least in part. Consider discussing this with a dentist first, especially with the bleeding gums.

  25. Leyla says:

    serious problem with my breath*

  26. Jazz says:

    I’m 16 years old girl I have this problem since 2017 feb it’s very much embarrassing my breath smells like poop even after i brush it a lot I don’t know what to do, am I gonna stay like this forever I have no future ?

    • cliffmaurer says:

      Hi there –
      I’m so sorry to hear you’re having the problem. Please consider scheduling a visit either in person or over telemedicine with one of our functional medicine practitioners. You can schedule by calling 773-296-6700.

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Far and away, the commonest phone call/e mail I receive asks about COVID-19 diagnosis.
Just print this out, tape it on your refrigerator door, and stay calm.


• Runny nose
• Sneezing
• Red, swollen eyes
• Itchy eyes and nose
• Tickly throat
• No fever

• Runny nose
• Sneezing
• Sore throat
• Mild muscle aches
• Mild dry cough
• Rarely a low fever

• Painful sore throat
• Hurts to swallow
• Swollen glands in neck
• Fever

FLU (Standard seasonal flu)
• Fever
• Dry cough (no mucus)
• Sudden onset over few hours
• Headache
• Sore throat
• Fatigue, sometimes quite severe
• Muscle aches, sometimes quite severe
• Rarely, diarrhea

• Shortness of breath
• Fever (usually above 100 degrees)
• Dry cough (no mucus)
• Slow onset (2-14 days)
• Mild muscle aches
• Mild fatigue
• Mild sneezing

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