When we think about flu, we usually think about the obvious symptoms: a fever, aching muscles, a cough, a blocked nose and the overwhelming desire to stay under a duvet for a few days. Your gut probably isn't the first thing that comes to mind.
But researchers are becoming increasingly interested in what happens inside the gut when the respiratory system is fighting an infection, and how your gut microbes influence the response of your immune system.
It sounds surprising, but your lungs and your gut may be more connected than you realise. This relationship is often called the gut-lung axis: a two-way communication system linking the microbial communities in the gut with the immune environment of the respiratory tract.1
And during flu season, that connection becomes particularly interesting.
Your immune system doesn't work in isolation
Your immune system is constantly interacting with the microbes that live in and on your body. A large proportion of immune activity is associated with the gastrointestinal tract. There, the immune system encounters an enormous number of microbial activities every day. Rather than simply helping with digestion, gut microbes produce compounds that can interact with immune cells and influence immune activity throughout the body.2
One important group is short chain fatty acids (SCFAs). These are produced when certain gut microbes ferment dietary fibre and other carbohydrates that escape digestion in the small intestine.3
The important point is, what happens in your gut doesn't necessarily stay in your gut.
Research into the gut-lung axis suggests that microbial products and immune signals can influence tissues elsewhere in the body, including the lungs.4
So, what happens to the gut when you get the flu?
Respiratory infections can be accompanied by changes in the gut microbiome. Research into influenza has identified differences in gut microbial communities during infection. Wider research into respiratory viruses also suggests that infection and changes in the gut microbiome can occur alongside changes in immune function.5
But scientists are still working out exactly what comes first. Does an infection change the microbiome, does the existing microbiome influence how someone responds to infection, or do both happen at the same time?
The answer is likely to be more complicated than a simple cause and effect relationship. Illness itself can change what we eat, how active we are, our sleep, stress levels and medication use, all of which can also affect the microbiome.6
So, while the gut-lung connection is fascinating, we can't currently say that having a particular gut microbiome will protect you from flu.
Meet the gut-lung axis
Think of your gut and lungs as two separate ecosystems that are in constant communication. Both are exposed to the outside world, and both interact closely with the immune system. When something changes in one environment, it can potentially influence the other.
Microbial metabolites, immune signals and changes in the body's inflammatory environment can all contribute to the conversation between the gut and respiratory system. This is one reason the microbiome is increasingly being viewed as part of a much larger biological network rather than something concerned only with digestion.1,7
Could your gut microbiome affect your response to flu?
There is growing evidence that the gut microbiome can influence immune responses to respiratory viral infections. Research suggests that gut microbes and the compounds they produce can communicate with the immune system and may influence antiviral responses in the lungs.8
Animal research has provided particularly interesting insight, including evidence that microbial metabolites can influence antiviral immune pathways. Human research is growing too, but it is much harder to establish whether differences in the microbiome actually cause differences in infection or disease severity.1
For example, people with respiratory infections can have different gut microbial communities from healthy people. This however doesn't automatically mean the microbiome caused the difference. The infection itself, along with changes in diet, medication, sleep and other factors, may also alter the microbiome.8
So, although the gut-lung connection is an exciting area of research, we aren't yet at the stage where your gut bacteria can predict whether you'll get flu or how severe it will be.
What about probiotics?
This is where flu season marketing can get ahead of the science. You may see probiotics promoted as a way to "boost your immune system" or prevent respiratory infections.
There is research investigating whether particular probiotic strains can influence immune responses and respiratory infection outcomes. However, probiotics are not one single treatment. Different strains can have very different effects, and evidence from one strain cannot automatically be applied to another.9
Research into microbiome based approaches for respiratory infections is promising, but it is still an emerging field.
What can you do for your gut during flu season?
You don't need a complicated "immune boosting" protocol. Some of the most sensible ways to support a diverse and resilient gut microbiome are remarkably ordinary.
1. Keep fibre rich foods on the menu.
Vegetables, fruit, beans, lentils, nuts, seeds and wholegrains provide different types of fibre and other compounds that gut microbes can use. Different microbes prefer different food sources, which is one reason dietary variety matters.3
If you're unwell and your appetite disappears, don't force yourself to eat a huge salad or bowl of lentils. As your appetite returns, gradually getting back to a varied diet can help restore your normal eating pattern.
2. Think variety, not superfoods.
Instead of focusing on one "superfood", think about variety across the week: different vegetables, fruits, pulses, nuts, seeds and wholegrains where tolerated.
Your microbes are a diverse community, and different species use different nutrients. The goal isn't perfection. It's giving your microbial ecosystem a range of raw materials to work with.
3. Don't forget fluids and rest.
Flu can leave you feeling exhausted and dehydrated, particularly if you have a fever. The NHS recommends drinking plenty of fluids when you have flu.10
And while you may be tempted to push through illness, rest and recovery matter too. When you're fighting an infection, your body is already doing a lot of work. Allowing yourself time to recover is more sensible than trying to exercise your way through it.
What we still don't know
The gut-lung axis is an exciting area of microbiome research, but there is still a lot we don't understand. We don't yet know whether deliberately changing the gut microbiome can reliably prevent influenza or improve recovery in humans. We also don't know exactly which microbial communities or metabolites matter most.
Future research may eventually help answer these questions. For now, the most useful takeaway is much simpler:
Your gut is not an isolated digestive tube.
It is a living ecosystem that interacts continuously with your immune system, and those interactions may extend all the way to the respiratory tract.
The bottom line
Flu might start as a respiratory infection, but your body's response doesn't happen in isolation. Your gut microbiome is part of a much bigger network involving your immune system, metabolism and other microbial ecosystems throughout the body.
We still have plenty to learn about exactly how this relationship works. But the emerging science gives us another reason to think about microbiome health as part of long term resilience, rather than something to "fix" when flu season arrives.
You don't need to wait for flu season to start looking after your microbiome.
A varied diet, plenty of fibre rich plant foods, adequate fluids, good sleep and sensible recovery habits are useful foundations all year round.
And when flu season arrives, the basics still matter most: good hygiene, staying home when you're unwell and giving your body time to recover.
