Probiotics for Canker Sores — What the Research Actually Shows

TL;DR

The idea behind probiotics for canker sores is reasonable: people with recurring canker sores have measurably different bacteria in their mouths than people without them. But the trials so far are small and don't agree. A 2020 review of seven randomized trials found that probiotics reduced pain compared with placebo but didn't make ulcers less severe, and they worked better as an add-on to steroid treatment than on their own (Cheng et al., 2020 — Sci Rep). The one placebo-controlled trial of an L. reuteri lozenge, taken for three months to prevent outbreaks, found no difference from placebo (Pedersen et al., 2020 — PMID: 31410765). Probiotics are generally safe, so trying one won't hurt most people. But they belong after the things with better evidence: testing B12, iron, folate, and zinc, and switching to SLS-free toothpaste.

Why Anyone Thought Probiotics Might Help

Canker sores happen when the immune system attacks the lining of the mouth. Bacteria live on that lining all the time, and the immune system is constantly deciding how to react to them. So it's natural to wonder whether the wrong mix of bacteria could push the immune system toward attacking, and whether adding "good" bacteria could calm it down.

There's some support for the first part. Several studies have compared mouth bacteria in people with and without recurring canker sores:

• In 60 people with canker sores and 60 matched controls, the bacterial communities on the inside of the cheek were different between the two groups, most clearly when people had active sores. No single "bad" bacterium stood out (Bankvall et al., 2014 — PMID: 25626771).
• A smaller study found people with canker sores had fewer Streptococcaceae and more of several other bacterial families than controls (Hijazi et al., 2015 — J Dent Res).
• Another found that overall bacterial diversity was the same, but people with canker sores varied more from one another (Kim et al., 2016 — BMC Microbiol).

What these studies can't tell you is which way it runs. An open sore changes the environment in the mouth, so the bacterial differences could be a result of canker sores rather than a cause. And none of them point to one specific bacterium that a probiotic could add or replace.

What the Probiotic Trials Found

There aren't many, and they test different strains, different products, and different goals, which makes them hard to compare.

Preventing outbreaks

The L. reuteri lozenge trial. Twenty people with recurring canker sores took either a lozenge containing two L. reuteri strains or a placebo lozenge twice a day for 90 days. Outbreak severity went down in both groups, and there was no significant difference between them (Pedersen et al., 2020 — PMID: 31410765). It's a small trial, so it could have missed a modest effect. But it's the most direct test of the idea that a daily L. reuteri lozenge prevents canker sores, and it didn't show a benefit.

A children's trial. In a study that included 60 children, lozenges containing L. acidophilus and B. lactis taken for five days during an outbreak led to fewer outbreaks over the following six months, though the effect on the sore itself was modest (Aggour et al., 2021 — Clin Oral Investig).

Treating an active sore

Pain relief. In the same study, adults who took the lozenges during an outbreak had less pain than controls at every check-in (Aggour et al., 2021 — Clin Oral Investig).

A topical L. reuteri gel. In a double-blind trial of 60 people, an L. reuteri gel applied three times a day for a week shrank ulcers and reduced pain more than an analgesic mouth rinse did (Samiraninezhad et al., 2023 — PMID: 38114936). This was a specially formulated gel, not a product you can buy, and it was compared with a rinse rather than a placebo.

Behçet's disease. In an open study of 23 people with Behçet's disease (which causes severe mouth ulcers), lozenges containing Lactobacillus brevis CD2 taken six times a day for a week reduced the number of ulcers, and the effect lasted about a week after stopping (Tasli et al., 2006 — PMID: 17067433). There was no control group.

Putting it together

A 2020 systematic review pulled together seven randomized trials. Probiotics reduced pain compared with placebo but didn't reduce ulcer severity, and they did better as an add-on to steroids than as a treatment by themselves (Cheng et al., 2020 — Sci Rep).

So the fairest summary: there's a weak signal that probiotics can ease the pain of an active sore, mixed evidence on prevention, and the single best test of daily L. reuteri for prevention was negative.

Why the Trials Are Hard to Compare

One reason the evidence is so murky is that "probiotics" isn't one thing. The trials above used different species, different strains within those species, different doses, and different ways of taking them: lozenges dissolved in the mouth, a gel put directly on the sore, and capsules swallowed for the gut. Some tested prevention over months. Others tested a week of treatment during an active sore.

Probiotic effects tend to be specific to the strain. A result for L. brevis CD2 tells you very little about L. reuteri, and a gel made in a lab tells you little about a chewable tablet from a pharmacy. So when a supplement label or article says "probiotics help canker sores," the right question is: which strain, in what form, tested how?

Mouth Probiotics vs. Gut Probiotics

Most probiotic supplements are capsules you swallow, meant to settle in the gut. Oral probiotics are usually lozenges or chewable tablets that dissolve slowly in your mouth, with the idea of getting bacteria onto the lining of the mouth directly.

For canker sores, the trials that showed any benefit mostly used products that dissolve in the mouth or go directly on the sore. There's a broader theory that gut bacteria influence the immune system throughout the body, including the mouth, and that's an active area of research. But no trial has shown that a swallowed gut probiotic reduces canker sores.

If you're going to try one specifically for canker sores, a lozenge or chewable that dissolves in the mouth matches what was actually tested better than a capsule does.

Reading a Probiotic Label

If you decide to try one, a few things on the label tell you whether you're getting what you think you're getting:

• The full strain name, not just the species. "Lactobacillus reuteri DSM 17938" is specific. "Lactobacillus reuteri" or "proprietary blend" isn't.
• The count of live bacteria at the expiration date, not "at time of manufacture." Bacteria die off on the shelf.
• Storage instructions. Some need refrigeration. A product that should be refrigerated and has been sitting in a warm warehouse may not contain much that's alive.
• The form. For the mouth, a lozenge or chewable. For the gut, a capsule.

More strains and a bigger number on the label don't make a product better. The strains in the trials were specific and the doses were modest.

Probiotics After Antibiotics

Some people notice canker sores during or after a course of antibiotics. Antibiotics do shift the bacteria in the mouth and gut, so it's a reasonable thing to wonder about, though no study has looked at it directly. Other things often happen at the same time, too: being sick, sleeping badly, eating differently.

If you tend to get sores after antibiotics, it's a reasonable time to try a probiotic, since it may help with antibiotic-related stomach upset as well. Just keep your expectations modest for the canker sores themselves.

What L. reuteri Does Have Evidence For

L. reuteri gets a lot of attention, and it does have real evidence in a few areas. Just not for canker sores yet.

• Infant colic. One strain (DSM 17938) reduced crying time in breastfed babies with colic by about 25 minutes a day more than placebo, in a pooled analysis of 345 infants (Sung et al., 2018 — PMID: 29279326).
• Gum disease, alongside a dental cleaning. In a small trial of people with periodontitis, L. reuteri lozenges after scaling and root planing improved pocket depth more than cleaning alone (Teughels et al., 2013 — PMID: 24164569).
• Gum health claims. On the other hand, in 2020 the European Food Safety Authority rejected a claim that the BioGaia Prodentis lozenge supports normal gum function, because a cause-and-effect relationship hadn't been established.
• IBS. The evidence is thin: one trial with a different strain combination, and no pooled analysis.

If you've seen L. reuteri described as "proven" for mucosal immunity or gut health in general, that's going further than the research does.

Is It Safe?

For most people, yes. Probiotics like L. reuteri have been given to infants, children, and adults in many studies with few side effects beyond occasional temporary bloating or loose stools.

The exception is people with a seriously weakened immune system: those on chemotherapy, after an organ transplant, on high-dose immunosuppressants, or with a central venous catheter. Rare bloodstream infections from probiotic organisms have been reported in these groups. If that's you, ask your doctor before taking any live probiotic.

Should You Try It?

Probiotics aren't where we'd start. These come first, because they have better evidence:

1. Get tested for B12, ferritin (iron), folate, and zinc. Deficiencies are common in people with recurring sores, and B12 has a placebo-controlled trial showing fewer outbreaks (Volkov et al., 2009 — PMID: 19124628).
2. Switch to an SLS-free toothpaste. Cheap, easy, and supported by evidence.
3. Look at your sleep, stress, and food triggers. See Sleep and Canker Sores and Stress and Canker Sores.

After that, a probiotic is a reasonable thing to try if:

• You've covered the basics above and still get frequent sores
• You also have gum problems, where L. reuteri has some evidence
• You've had a lot of antibiotics recently
• You simply want to try it and are comfortable with "probably won't hurt, might help a little"

If you do try it, give it a fair test. Take it daily for at least three months, keep a record of when sores appear, and don't change anything else at the same time. Otherwise you won't know whether it did anything.

The most widely available oral probiotic is BioGaia Prodentis, a chewable tablet containing two L. reuteri strains. You chew it slowly and let it dissolve rather than swallowing it whole, since the goal is to get the bacteria into your mouth. Taking it at bedtime, after brushing, keeps toothpaste and food from washing it away. Keep in mind that the only prevention trial of a two-strain L. reuteri lozenge for canker sores didn't find a benefit.

What About Yogurt and Kefir?

Fermented foods contain live bacteria, but the strains and amounts vary a lot, and none have been tested in a controlled trial for canker sores. If you like them, there's no reason to stop. If dairy is a trigger for you, though, they can make things worse. See Dairy and Canker Sores.