Can Oral Health Affect Your Gut Microbiome?

June 16, 2022 9 min read

Can Oral Health Affect Your Gut Microbiome? - Layer Origin Nutrition

How Prebiotics Impact Your Oral Microbiota?

The mouth is the first place your food goes before it meets its fate in the stomach and intestines. And it’s also the first place our microbiota greets that food, and the outside world.

We know the gut is a complex ecosystem consisting of millions of bacterial strains that keep digestion functioning well and clearing out potentially infectious bacteria. But we also take for granted where these bacteria come from.

The gut microbiome is initially populated at birth. Over time it matures from exposure to solid foods and various environmental factors like dirt and air. The mouth plays a huge role in this as it’s the first point of entry into our interiors. Oral bacteria generally stay put in the mouth, but they work to keep pathogenic bacteria out of the gut and help feed beneficial bacteria and even permit passage deeper into the gut.

  • Is there a good oral microbiota?
  • What contributes to the oral microbiota?
  • What happens when the oral bacteria go bad?

In this article we discuss the composition of the oral microbiota – both good and bad – and how it contributes to overall oral health. We also discuss the relationship between the gut microbiota and oral health, how antibiotics can impact oral health. We’ll also address how prebiotic and probiotics can help restore the oral microbiome and may even contribute to improved oral health.

Ecology of the Mouth

The oral microbiota plays a similar role in digestion, barrier defenses, and tissue health as that of the gut bacteria. In fact, the mouth is our microbiota’s first, and maybe most important, stand against pathogenic bacteria, viruses, and even yeast. Not only that, these bacteria act as groundskeepers to our teeth and gums.

It’s these unique features that make the oral microbiota so complex and fascinating. The bacteria in the mouth are able to withstand both external and internal environmental factors: the physical demands of foods and liquids, the ever-changing pH of saliva, and the introduction of competing bacteria from foods and the air that we breathe. They also mark the boundary between the outside and the internal processes of digestion.

The oral microbiota consists of bacterial phyla including Bacteroides, Actinobacteria, and Firmicutes1. Most of the genera in these groups are commensal and also found in the gut. But sometimes, some strains can grow out of control and unleash pathogenicity as they take over.

Let’s take a look:

Good Oral Bacteria

The oral bacterial ecosystem is diverse and consists of strains such as Lactobacillus and Bifidobacteria. They interact with other strains to break down sugars, influence inflammatory responses, and even communicate with the bacteria in our guts.

Lactobacillus is one strain that gets a lot of credit for protecting the mouth and preventing the growth of pathogenic strains. Species such as L. casei, L. reuteri, and L. rhamnosus GG help to directly control growth of Streptococcusstrains. Lactobacillus actually has some pretty unique mechanisms to stop pathogenic bacteria – some strains produce ethanol and bactericidal compounds that destroy bacteria2.

These Lactobacillus strains, and even Bifidobacteria, also produce hydrogen peroxide that is another powerful anti-bacterial compound that aids in oral health by killing pathogenic bacteria.

So, we know that these, and other, strains are important in maintaining oral health. And we now know we can promote their growth through probiotic and prebiotic supplements, just like adding yogurt or HMO’s to your diet for gut health.

There are some prebiotic supplements that consist of sugars like arabinose that are substrates for Lactobacillusand other oral bacteria that help promote oral wellness. There are also probiotic foods and even toothpastes that contain these and other beneficial strains. More on that later. Next let’s discuss pathogenic bacteria and their impact on oral health.

Bad Oral Bacteria

Poor oral health is the result of many factors like not brushing or flossing (ugh), or issues like tissue damage and inflammation. But ultimately, oral health comes down to the balance of good and bad bacteria.

Not brushing and flossing allows food particles to collect on the teeth and gums. This contributes to tissue damage and inflammation which allow pathogenic bacteria to thrive.

There are a number of pathogenic bacteria that cause a range of issues in the mouth. The most common, and pathogenic, strain is P. gingivalis, which – together with Fusobacterium nucleatum – causes halitosis (bad breath) during the breakdown of various amino acids2. P. gingivalis is the prime culprit in gingivitis, or gum disease. Gingivitis is a very common, treatable disease wherein bacteria invade and erode gum tissue and elicit chronic inflammation. Gingivitis can become a serious dental emergency if left untreated though.

Other common pathogenic bacteria include Actinobacteria, Streptococcus mutans, H. pylori, and the yeast Candida albicans. Candidiasis is a yeast infection that can be very painful and last a long time if C. albicans is allowed to thrive.

Actinobacteria and S. mutans can also contribute to serious gum disease and even conditions like bacteremia, which is when bacteria are able to enter the bloodstream. This is not common but is usually the result of a high abundance of pathogenic bacteria in the mouth that is able to invade gum tissue and, eventually, circulation. S. mutans is also implicated in endocarditis and heart disease3,4. No need for concern yet – this is still poorly understood, but it illustrates how the mouth can be an ideal portal for pathogenic bacteria to gain a foothold.

Another example of this is H. pylori – this strain is implicated in gastric ulcers; it is believed to originate in the mouth. While it’s hard to say, it seems likely that H. pylori is able to get into the gut when and take up residence where it can disrupt intestinal function and cause severe ulcers.

All these pathogenic bacteria are, for the most part, a part of oral microbiota, and under normal circumstances they contribute to good oral health. But they can become pathogenic under the right circumstances: poor diet, bad oral health, gum infections, and gut dysbiosis. While the gut and mouth are distinct, they are connected, and the health of one affects the health of the other.

Does Gut Dysbiosis Contribute to Oral Dysbiosis?

This is a sort of ‘chicken-or-the-egg’ question. Since the mouth leads to the gut, it can be assumed that what happens in the mouth, also happens in the gut. This is mostly true, except that the bacteria that cause dysbiosis or stomach infections tend to make it right past the mouth without any notice. These bacteria, like Clostridium and E. Coli, prefer the intestinal environment. They aren’t really prone to getting stuck in the mouth and living there.

Bacteria like Streptococcus and Actinomyces live happily in the mouth. If their numbers grow too large, they can overcome other bacteria and travel into the airway and even blood. This is actually pretty common and has been widely accepted as a primary driver of upper-respiratory infections and even bacteremia.

But as far as gut dysbiosis is concerned, it seems that the bacteria in your mouth can’t really survive the harsh and oxygen-deficient intestines. So, it’s more likely that gut dysbiosis offsets the oral microbiome by preventing commensal bacteria from thriving and inhibiting crucial immune processes.

One thing that seems to influence the oral microbiota is sugar – oligosaccharides and other sugars found in food can influence which bacteria grow in your mouth.

Too Much Sugar Can Rot Your Teeth, Right?

Well kind of…but the sugar isn’t the problem, it’s what eats the sugar.

Bacteria generally thrive off sugars – usually from indigestible fibers or complex oligosaccharides. This goes for both the oral and gut microbiota.

But there are differences in the sugars these bacteria eat and their effects.

The main bacteria in the gut – Bifidobacteria and Lactobacillus – prefer a diet of the prebiotics fructo- and galacto-oligosaccharides, and also fucosyllactose - the sugars typically found in human milk oligosaccharides. The bacteria in the mouth also prefer the same types of sugars.

These sugars are unique – they’re effectively indigestible and some bacteria have developed unique mechanisms to consume them that allows them to outcompete other strains. This unique feeding mechanism is actually the driver of bacterial diversity and the inhibition of pathogenic bacterial growth.

Bifidobacteria and Lactobacillus in the mouth also consume arabinose, xylitol and xylose – these are relatively simple sugars found in many foods and sweeteners that we consume. But they act as prebiotics to a degree, and promote salivary flow, both of which promote bacterial growth5.

There are other, simpler sugars from our diet – fructose and sucrose – that tend to be not so great for oral health. In the gut, these sugars are eaten by non-picky eaters which also happen to proliferate quickly and outpace commensal bacteria.

Diets high in simple sugars can contribute not only to metabolic disorders, but can drastically alter the structure of the gut and oral microbiomes6. Too much sugar in the diet can promote the growth of pathogenic bacteria in the mouth, and we know this can lead to cavities, gingivitis, and more serious things like infection or gut dysbiosis.

Oral Antibiotics and What They Do to Oral Bacteria

Antibiotics eliminate nearly all bacteria – in the gut and the mouth. We’ve all taken them, maybe to fight an infection or before surgery. Antibiotics prevent serious infections from highly pathogenic bacteria, but they also completely wipe out our bacterial ecosystems. This includes oral antibiotics like chlorhexidine which are usually taken before oral surgery.

After a course of antibiotics your microbiota needs to be restored. Unfortunately, this can result in the early growth of pathogenic bacteria that cause serious gut distress, and others that can cause bad breath or odd tastes.

After a regimen of antibiotics, we should try to eat foods that help re-establish our gut and oral microbiota. Avoid strictly probiotic supplements since adding probiotics after antibiotic use might extend the recovery time for your gut microbiome according to a recent research published in Cell. You can read more here.

Your best bet is to eat pre-biotics that encourage the growth of the right bacteria. This includes high fiber and fermented foods. There are also supplemental human milk oligosaccharides – these are complex sugars that specific bacteria can metabolize and include 2’-fucosyllactose (which is what is found in breast milk and made available as supplements by fermentation). You can actually find these and related products here.

There are plenty of studies that demonstrate the how HMO’s can restore the gut and oral microbiota; in addition, there are some probiotic mouth rinses and toothpastes that will help to recolonize the mouth with the right bacteria, and you can use these with HMO supplements2,4,7.


Here we discussed the ecology of the oral and gut microbiota, and the impacts of antibiotics on these bacteria. Here’s a brief recap:

  • The bacteria in the mouth are similar to those in the gut but tend to thrive in lower diversity. These include Bifidobacteria and Lactobacillus
  • There are a number of commensal oral bacteria that can invade gum tissue and contribute to gum disease, tooth decay, and even airway infections and gut dysbiosis. This includes gingivalis and Streptococcus
  • Gut dysbiosis can also inhibit the growth of good oral bacteria
  • Sugar doesn’t cause cavities – bad bacteria cause cavities
  • Antibiotics wreak havoc on the gut and oral microbiomes and should be followed with prebiotic foods or prebiotic supplements
  • HMOs and prebiotic foods, and some probiotic toothpastes, can help replenish healthy gut and oral bacteria

The oral microbiome is just as important to overall health as the gut microbiome. It’s also just as sensitive to changes in diet. Too much sugar can promote bad bacteria.

But all is not lost – a good diet and a little help from some prebiotic HMO’s (and maybe good brushing habits) will go a long way in keeping the bacteria in your mouth happy and your smile beautiful! You can shop our PureHMO prebiotics here: 

Written By: 

Zach Pierce

Masters in Nutritional Biology with emphasis in Immunology; Certified Personal Trainer. 


(1)        Koliarakis, I.; Messaritakis, I.; Nikolouzakis, T. K.; Hamilos, G.; Souglakos, J.; Tsiaoussis, J. Oral Bacteria and Intestinal Dysbiosis in Colorectal Cancer. Int. J. Mol. Sci. 2019, 20 (17), 4146.

(2)        Nanavati, G.; Prasanth, T.; Kosala, M.; Bhandari, S. K.; Banotra, P. Effect of Probiotics and Prebiotics on Oral Health. Dent. J. Adv. Stud. 2021, 9 (1), 1–6.

(3)        Leishman, S. J.; Lien Do, H.; Ford, P. J. Cardiovascular Disease and the Role of Oral Bacteria. J. Oral Microbiol. 2010, 2 (1), 5781.

(4)        Reddy, R.; Swapna, L.; Ramesh, T.; Singh, T.; Vijayalaxmi, N.; Lavanya, R. Bacteria In Oral Health - Probiotics and Prebiotics A Review. Int. J. Biol. Med. Res. 2011, 2, 1226–1233.

(5)        Edgar, W. M. Sugar Substitutes, Chewing Gum and Dental Caries--a Review. Br. Dent. J. 1998, 184 (1), 29–32.

(6)        Keller, M. K.; Kressirer, C. A.; Belstrøm, D.; Twetman, S.; Tanner, A. C. R. Oral Microbial Profiles of Individuals with Different Levels of Sugar Intake. J. Oral Microbiol. 2017, 9 (1), 1355207.

(7)        Devine, D. A.; Marsh, P. D. Prospects for the Development of Probiotics and Prebiotics for Oral Applications. J. Oral Microbiol. 2009, 1 (1), 1949.

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July 16, 2022

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