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Bad Breath Can Start in the Stomach—Here’s How to Fix It

Written by Dr. Michael Ruscio, DC on May 9, 2025

Written by Dr. Michael Ruscio, DC on May 9, 2025 — Reviewed by Kellie Blake

• Bad Breath—Mouth or Beyond?|
• Gut-Mouth Connection|
• Bad Breath from the Stomach|
• SIBO and Bad Breath|
• Probiotics for Bad Breath|
• Other Fresh Breath Supports|

Bad breath, or halitosis, can chip away at confidence and make social interactions embarrassing. While most people assume that smelly breath is caused by poor oral hygiene, the root cause isn’t always in the mouth. Bad breath from stomach issues—or more accurately, from problems occurring a little further down the digestive tract—is more common than you’d think.

In this article, I’ll explore how small intestinal bacterial overgrowth (SIBO) and other microbiome imbalances can play a significant role in halitosis. We’ll also look at what natural treatments work, including how probiotics can offer real, lasting relief.

When my clients realize they can stop obsessively brushing, rinsing, or masking the issue with sprays and mouthwash, it can be such a relief. So let’s dive into why your gut might be the missing piece in your journey to fresher breath.

Is It Oral Hygiene—or Something Else? Uncovering the Source of Bad Breath

Food particles left in the mouth can decay, feeding oral bacteria that release foul-smelling sulfur compounds and contribute to periodontal disease.

But if you’re diligent about brushing, flossing, and rinsing, you’re already addressing this common cause of bad breath.

When bad breath lingers despite good oral hygiene, it is time to look to other sources. For an estimated one in ten people with halitosis, the mouth is not the origin at all 1. In these cases, the root cause often lies deeper—within the gastrointestinal tract.

The Gut-Mouth Connection

Around a quarter (26%) of all bacteria that live on or inside humans reside in the mouth 2, while 29% live in the gut 3. A 2021 review found that Firmicutes dominate the mouth, while the gut has more Bacteroidetes, highlighting their distinct microbial communities 3.

Normally, there’s a clear separation between the microbial inhabitants along the digestive superhighway. A healthy oral-gut barrier—made up of stomach acid, bile acids, and a strong gut wall—generally prevents mouth microbes from making their way into the gut, while good hygiene stops gut microbes from sneaking into the mouth 3 4 5. 

Similar protective mechanisms also stop bacteria in the large intestine from traveling upward into the small intestine. Stomach acid, healthy intestinal motility (peristalsis), and an effective ileocaecal valve between the small and large intestines all help maintain this balance.

The trouble starts when microbes begin freeloading in places they shouldn’t. This can happen due to poor motility, structural issues in the digestive system, or general imbalances in the microbiome, known as dysbiosis.

This microbial mingling has the potential to contribute to bad breath.

Bad Breath from the Stomach and Gut

Beyond the mouth, several wider conditions that are linked with microbiome imbalances can be responsible for persistent halitosis. These include: 

• Oral thrush 6
• Helicobacter pylori H. pylori 7
• IBS  8
• IBD (Crohn’s disease and ulcerative colitis) 9
• Different types of dysbiosis and leaky gut 10
• Chronic acid reflux (GERD) 11
• Type 2 diabetes 12
• Non-alcoholic fatty liver disease 13

However, among these potential causes, one stands out—SIBO, or small intestinal bacterial overgrowth. This specific type of dysbiosis is a particularly significant, yet often overlooked, contributor to breath odor. 

SIBO as a Cause of Bad Breath

SIBO is a type of dysbiosis in which bacteria that usually live in the large intestine (large bowel) start growing in large amounts in the small intestine, where they don’t belong. These out-of-place microbes can disrupt digestion, interfere with nutrient absorption, and—as growing research shows—can have a surprising effect on your breath.

A 2024 observational study revealed some striking findings. In the study, 162 people with both unexplained bad breath (idiopathic halitosis) and SIBO were given a daily probiotic for two months 14. After two months on probiotics:

• 80% of participants became SIBO-negative by the end of the study.
• 99% of those whose SIBO cleared reported significantly fresher breath.

Although research into the gut-breath connection is still in the early stages, other studies have drawn links between SIBO and halitosis in chronic health conditions. 

• In one study, 84% of people with inflammatory bowel disease (IBD) and SIBO reported bad breath 15. 
• In another study, 65% of metabolic dysfunction-associated steatotic liver disease (previously called non-alcoholic fatty liver disease) patients testing SIBO-positive also had halitosis 16.

How Does SIBO Cause Bad Breath?

One of the key ways SIBO may produce bad breath is through the production of dimethyl sulfide (DMS)—a volatile sulfur compound known for its unpleasant, slightly sweet odour, often compared to radishes or cooked cabbage 1. 

While hydrogen and methane (also produced by SIBO) are odorless, DMS tends to cause distinct bad breath that is often associated with gut issues.

Intestinal cells can’t break down DMS in the gut. Instead, it gets absorbed into the bloodstream, travels to the lungs, and is exhaled in the breath, bringing the bad smell with it 1.

Clinically, It’s Fair to Assume Bad Breath May Be Microbiome Related

When clients come to me with persistent bad breath that doesn’t appear to originate in the mouth, I often work from the assumption that a gut microbiome imbalance, most commonly SIBO, is playing a role.

And because probiotics are both helpful for SIBO and gentle enough to try first, they’re typically our go-to starting point for natural treatment.

Probiotic Protocol for Bad Breath

Probiotic supplements may help resolve SIBO by restoring a healthier balance of gut bacteria 14. In the past, we didn’t have the strong evidence we now do to support probiotics for SIBO, so practitioners were often cautious, concerned that adding more bacteria into an already overgrown gut might make things worse.

Now we know that probiotics are almost always beneficial. SIBO involves an overgrowth of the wrong types of bacteria, and probiotics help by competing with these unwanted microbes for space and nutrients. As a healthier gut balance is restored, there’s less fermentation by harmful bacteria in the small intestine, meaning fewer of the smelly volatile compounds that can be exhaled through the breath 14.

In the clinic, we use a multi-strain probiotic approach, which is supported by much of the latest research on SIBO. Case in point: the impressive results in the 2024 study we just discussed came from using a combination of probiotic strains, including Bifidobacteria and Lactobacilli.

Our tried-and-tested protocol involves using these three together:

• A Lactobacilli–Bifidobacteria blend
• A beneficial Saccharomyces yeast
• Soil-based probiotics

Here are the dosages and timings we’ve found work best in practice:

A great thing about this triple-therapy probiotic approach is that it covers so many bases—and it’s not just helpful for people whose bad breath is caused by SIBO. In fact, it can support a range of underlying causes of foul-smelling breath where microbiome imbalances are involved. 

Other Supportive Practices for Fresh Breath

For persistent bad breath, especially when it’s linked to microbiome imbalances like SIBO, additional strategies can really help. Of course, it also helps to limit the obvious bad breath culprits, particularly garlic and onions.

A Low FODMAP Diet

FODMAPs are fermentable carbohydrates that certain bacteria in the gut love to feed on. When these bacteria ferment FODMAPs, they can overgrow, produce gases and other byproducts that potentially contribute to bad breath.

There’s strong evidence for using a low FODMAP diet to manage irritable bowel syndrome (IBS), and research is growing around its use for SIBO as well (it’s worth noting that IBS and SIBO often coexist).

One randomized controlled trial found that a low FODMAP diet reduced SIBO symptoms and bacterial overgrowth after just two weeks 17. 

Our Low FODMAP Diet Plan guides you through which foods to limit and how to gradually reintroduce higher FODMAP foods over time to test your tolerance in a structured way.

Consuming Fermented Foods

A 2021 study showed that eating six servings of fermented foods daily improved microbiota diversity and reduced inflammation in healthy people 18. That’s promising, but it’s worth noting that we don’t yet have results specific to people with SIBO.

Even so, many of my clients with various forms of dysbiosis find that fermented foods—especially when they can’t tolerate high-fiber diets—can help with gut symptoms, including bad breath. For those who struggle with fiber-rich plant foods (often recommended to support the microbiome), fermented options can be a gentler, more digestible alternative.

That said, if you have sensitivities to FODMAPs, not all fermented foods may be suitable. It’s often a case of testing and finding your own preferences and tolerances.

Here’s a quick guide that may help 19:

Lower-FODMAP fermented foods: 

• Goat’s milk yogurt
• Pickled gherkins
• Tempeh
• Spelt sourdough bread
  

Higher-FODMAP fermented foods:

• Kefir
• Pickled vegetables (kimchi)
• White cabbage sauerkraut (red cabbage sauerkraut is moderate FODMAP)
• Standard cow’s milk yogurt

3 pro tips for searching out the best fermented foods:

1. Choose refrigerated (not shelf-stable) types
2. Choose those that are unpasteurized
3. Look for ”live active cultures” on the label

An Elemental Diet

In stubborn cases of halitosis, an elemental diet—a liquid dietary formula absorbed quickly in the small intestine—can reset the gut by depriving bacteria of fuel.

For a full resolution of gut overgrowths like SIBO and Candida, we recommend a one to three-week elemental diet program with all meals replaced by elemental formula. However, there are a couple of caveats here. First, this long period on a liquid-only diet needs practitioner support—don’t attempt it on your own. And second, I recommend that people with oral Candida, or thrush, don’t drink the elemental diet shakes. My concern is that the easily absorbed carbs might feed fungi or microbes in the mouth, though no research confirms this risk.

Elemental Heal is the product we recommend to our clients. It tastes good, provides all the nutrients needed, and comes in standard, whey-free, and low-carbohydrate versions.

Antimicrobials and Prokinetics

Antimicrobials—such as rifaximin, oregano oil, or berberine—can sometimes be helpful alongside probiotics to target harmful microbes, SIBO, and broader dysbiosis.

Prokinetics may also support recovery in people with persistent SIBO by improving gut motility and preventing bacterial stagnation. These can be herbal formulas like Iberogast, or prescription medications such as prucalopride or metoclopramide.

That said, antimicrobials and prokinetics are usually only necessary if probiotics and dietary changes don’t move the needle on gut symptoms, including bad breath.

Fresh Breath May Start in the Gut

If you’ve been struggling with chronic bad breath and nothing in your dental routine seems to help, it might be time to look a little deeper—into your gut. SIBO and other types of dysbiosis can produce smelly volatile compounds that make their way into your breath.

The good news? You’re not stuck with it. Starting with probiotics and dietary changes, it’s possible to rebalance your microbiome and feel confident about your breath again.

Indeed, fresher breath could be a sign that your whole gut health is turning a corner. 

If you’re interested in a wider approach to improving gut health, I outline a structured 8-step plan in my book Healthy Gut, Healthy You. For more personalized help with gut-related health problems, you can also book an appointment with us at the Ruscio Institute for Functional Health.

The Ruscio Institute has also developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.