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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
    https://store.wholehealthchicago.com/shop/periobiotic-toothpaste/

  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
    http://www.rvcrx.com/

  11. Renee Keogh says:

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

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