When we think about protecting ourselves during flu season, we usually think about vaccines, handwashing, avoiding sick people and getting enough sleep.
But there is another ecosystem sitting right at the entrance to your body that rarely gets mentioned: the microbiome in your mouth.
Your mouth is home to hundreds of different species of bacteria, along with fungi, viruses and other microorganisms. Together, they form a complex community known as the oral microbiome. Far from simply being something we need to get rid of, many of these microbes are normal and potentially beneficial members of our body's ecosystem.1
So, what happens when the flu arrives? And could the balance of bacteria in your mouth influence how your body responds?
Your mouth is more than the gateway to your stomach
Every day, we swallow saliva containing huge numbers of microorganisms from our mouth. Most of the time, this is completely normal. Our oral microbiome is part of the microbial environment we live with every day.
But the mouth is also connected directly to the respiratory tract. We breathe through it, cough through it and inhale tiny droplets and particles through it. This creates an interesting relationship between the oral microbiome and respiratory health.
Research increasingly suggests that microorganisms in the mouth and upper airways can interact with respiratory viruses and with the immune system. During influenza infection, for example, the microbial communities in the upper respiratory tract can change considerably.2
This doesn't mean that particular bacteria simply "cause" flu. Influenza is caused by influenza viruses. The more interesting question is whether the microbial environment surrounding the virus can influence what happens next.
Does poor oral hygiene increase your chances of catching flu?
This is where things get interesting. You may have seen claims that poor oral hygiene makes you more likely to catch flu or causes respiratory infections to become more severe.
There is some evidence pointing in this direction, but it is not strong enough to say that poor oral hygiene causes influenza.
One human study found that people with poorer oral hygiene appeared more likely to have influenza infection, with an estimated 63% higher odds. However, the confidence interval was wide, and the result did not quite reach conventional statistical significance.3
So, rather than saying "bad oral hygiene causes flu", the more accurate conclusion is that the condition of the oral environment may be one factor worth investigating in respiratory infections.
And there are some fascinating clues about why it might matter.
Your oral bacteria aren't all the same
A healthy microbiome isn't a mouth containing no bacteria. It's a diverse microbial community living in a relatively stable ecosystem.
Problems can arise when this ecosystem becomes disrupted. Poor oral hygiene can allow dental plaque, a biofilm containing bacteria, to accumulate. This can contribute to gum disease and inflammation. Some oral bacteria can also interact with viruses.4
Influenza virus, for example, relies on an enzyme called neuraminidase to help newly produced virus particles leave infected cells and spread. Laboratory research has found that substances produced by some oral bacteria can affect this process.5
This is intriguing, but it is important not to jump from a laboratory finding to "these bacteria make you catch flu". The human body is much more complicated than a dish of cells.
The surprising role of saliva
Your saliva isn't just there to keep your mouth wet. It contains proteins, enzymes and other molecules that contribute to the mouth's defence system. Some of these have antiviral properties.6
In 2025, researchers investigated whether toothbrushing could influence saliva's ability to inhibit influenza virus. In a small study involving just 16 adults, saliva collected shortly after toothbrushing showed increased anti-influenza activity compared with samples taken before brushing. The effect was temporary, and the researchers found that greater amounts of bacteria in mouth-rinse samples were associated with lower antiviral activity.7
This is an interesting finding. But it doesn't mean brushing your teeth is an influenza treatment or that brushing prevents you from catching the flu. What it does show is that the oral environment is biologically active, and that changing that environment can influence properties of saliva.
Flu can affect the microbial ecosystem too
The relationship doesn't necessarily go in one direction. It's not simply that your microbiome might influence an infection. The infection can change the microbiome too.
Studies following people with influenza have found substantial changes in the microbial communities of the upper respiratory tract during infection. As people recovered and the virus was cleared, the microbial community moved back towards its previous state.8
This is an important concept when we think about microbiomes. They are ecosystems and not fixed collections of bacteria.
A virus can disturb the environment, and changes in the environment can alter which microbes thrive. Those changes may also influence how the body responds to subsequent challenges.
Researchers are particularly interested in this because influenza can sometimes be followed by secondary bacterial infections. Influenza can damage respiratory tissues and alter immune responses, making it easier for certain bacteria to establish themselves.9
This is one reason the relationship between viruses and bacteria is much more complicated than simply "good bacteria versus bad bacteria".
Myth vs reality
Myth: A high level of bacteria in your mouth means you're more likely to catch the flu.
Reality: Your mouth naturally contains a huge and diverse microbial community. The important question isn't simply how many bacteria are present, but which microorganisms are present, how they interact and how stable the ecosystem is.10
Myth: Brushing your teeth can stop you getting the flu.
Reality: Regular brushing is essential for oral health, and emerging research suggests it can temporarily influence saliva's anti-influenza activity. But we don't yet have evidence that brushing prevents influenza infection.7
Myth: The answer is to kill as many bacteria as possible.
Reality: The goal of microbiome health isn't to create a sterile mouth. It's to support a healthy oral environment and prevent excessive plaque accumulation and gum inflammation.11
So, what should you actually do?
The good news is that the basics haven't changed.
1. Brush twice a day. The NHS recommends brushing for around two minutes, twice a day, with fluoride toothpaste.12
2. Clean between your teeth. Floss or use interdental brushes daily to remove plaque from areas your toothbrush cannot reach.
3. Don't ignore bleeding gums. Bleeding, swollen or sore gums can be signs of gum disease and are worth discussing with a dentist.
4. Think ecosystem, not sterilisation. Your mouth is supposed to contain microorganisms. The aim is to maintain a healthy microbial environment rather than trying to eliminate every bacterium.13
5. Keep the bigger picture in mind. Oral health is only one part of respiratory health. Vaccination, sleep, nutrition, hand hygiene and avoiding exposure to infection remain important ways of reducing your risk from flu.
Did you know?
Your mouth and gut aren't separate microbial worlds.
Every day, microorganisms from your mouth travel down into your digestive system, creating a continuous connection between the two ecosystems. Researchers now refer to this as the oral-gut microbiome axis.14
And that brings us to another fascinating question: if the microbes in your mouth can interact with what happens in your airways, what about the trillions of microbes living further down in your gut?
That's where the story gets even more interesting.
