Revised 10/09/2025
During cold and flu season, you may be wondering how to help support and boost your natural immunity. The latest science illustrates that our innate immunity relies on a healthy gut microbiome.
So, how do you support your gut microbiome to help strengthen your immunity? We asked our scientists, researchers, and physicians at Viome Life Sciences to share ways to boost immunity and the gut-immune system connection.
The key role your microbiome plays in immunity
Our bodies are far from a microbe-free environment. Rather, the reality is our bodies are full of caverns rich in microscopic organisms that help us maintain internal homeostasis and immunostasis – often by interacting with our immune cells.
The gut microbiome aids in orchestrating these communications. Depending on the balance and fitness of the gut flora, our immune response can prove to be strong and resilient, or weak and late to the game. Nurturing our gut ecosystem can be one of the most profound ways we can beef up our immune response.
When dysfunctional, your gut microbiome can cause unintentional harm when performing its normal tasks, like a dull knife. However, when kept in fit condition, it performs seamlessly and precisely with less risk to surrounding areas. In this manner, a healthy gut microbiome functions well and is less likely to harm your intestinal lining - the thin barrier that keeps microbes safe and sound in their preferred environment - your gut - and keeps them from exploring other areas we don’t want – like in your blood!
When the intestinal lining is compromised, our gut microbes can escape and wind up in places they don’t belong, like other organs. As they accrue in these areas, the toxins and metabolites they secrete can lead to inflammatory reactions that damage these tissues and lead to more harm to the body. This is one of the many reasons why we believe so strongly in re-establishing a healthy gut lining. But it also plays a role in managing our immune response in times of infection.
Many commensal - or beneficial - microbes help to maintain the health of the gut lining. This can be from metabolizing fiber to produce butyrate, a healthy food for our gut lining cells, to competing with pathogens for space. When our gut microbiome has a healthy butyrate production, it helps our intestinal lining stay strong and remain intact. Conversely, our gut lining returns the favor by protecting many of these commensal bacterial communities when pathogens are sensed. In fact, our immune cells can be so “smart” that they recognize special peptides on the outside of beneficial bacteria(1) that signal to the immune cells they’re safe and not foreign at all. Convenient, isn’t it?
This is just one of many ways our friendly gut microbes help us fight invaders. Additionally, when their populations are strong, they also out-compete for space! Many invaders prefer special sites of attachment on our gut lining cells. With a healthy, diverse microbiome – these sites are taken up, leaving invaders with few places to settle(2).
Fighting off viruses
When it comes to viruses, bacteria are much like us. They, too, are susceptible to viral infections and employ unique ways to keep them and their environment healthy. When the populations of beneficial microbes are balanced and strong, it can be easier for them to communicate among each other when they sense a new viral pathogen. This communication, called quorum sensing, helps them react faster to their own immune defense(3). Once they respond they retain “memories” of their viral defense mechanisms in their genetic code, passing on their immunity to future generations. This translates to healthy commensal populations that are less likely to be wiped out from viruses, impacting the health of our gut.
A healthy microbiome = healthy immune response
Keeping your gut microbiome healthy and functioning optimally is key in supporting a healthy, robust immune response. You can see this when you are able to fight off seasonal challenges easily in a few days.
Having a healthy gut microbiome is something that you absolutely can assist. When you eat foods that are high in nutrients, including vitamins, minerals, probiotics and prebiotics, your microbiome is able to maintain a large variety of microbes that produce substances that are helpful to your gut, rather than harmful substances that tax your digestive system and weaken immunity.
Gut barrier health
The inner lining of the small and large intestines (called the gut barrier) facilitates the uptake of nutrients, water, and electrolytes, and keeping out pathogens. It can be vulnerable as it consists of only a single layer of human cells. When our gut barrier is healthy, it acts as one of the first lines of defense.
When your gut barrier is compromised, things from the outside environment, such as toxins, medications, and harmful bacteria can make their way into your bloodstream and negatively affect your immune system, inflammation levels, digestive health, and overall well-being. Viome’s Gut Intelligence Test™ and Full Body Intelligence Test™ have an Intestinal Barrier Health score to measure this.
It’s all about balance
So as you can see, it’s important to have balance within your gut microbiome. Balance means that the microbes in your gut produce lots of healthy substances with the food you feed it, and not an overabundance of harmful, inflammatory substances. A healthy microbiome is high in richness—the variety of different active microbes present, and diversity—how evenly (or not) their activity levels are distributed throughout.
As we mentioned, approximately 70-80% of your immune system resides in the lining of your gut. When you have high richness and diversity in your microbiome, your immune response is more capable and stable.
Foods to avoid
While there is no single healthy diet, several food types, when eaten to excess, can cause harm to your gut microbiome. If you are experiencing digestive issues or other health problems, it could be related to your microbiome, these include:
- Sugary food. Diets with high sugar content enable unhealthy bacteria to thrive inside the gut, causing weight gain and other health conditions.
- Artificial sweeteners like saccharin or aspartame, reduce good bacteria in your gut and can lead to high levels of blood sugar.
- Unhealthy fats. While fats like Omega 3 help the good gut bacteria, saturated fats can cause bad bacteria to thrive.
- Processed or cured meats contain not only high amounts of sodium, but also flavorings, preservatives, and chemicals, including nitrites that are known to be unhealthy.
Boosting immunity through nutrition
Food is one of the first tools you have in your toolbox to help support your innate immunity, since a healthy gut means a stronger immune response.
But then, the next question is: Which foods? How much? How often?
There are long lists of foods nutritionists automatically recommend to help boost immunity. Oranges, strawberries, and broccoli contain vitamin C to help increase blood levels of antibodies. Spinach, carrots, and apricots have beta carotene that helps antibodies fight toxins. Onions, garlic, and asparagus are rich in prebiotics. The fiber they contain is food for your gut microbes to produce short-chain fatty acids essential to gut health. Natural probiotic foods like unsweetened yogurt and some cheeses can assist by introducing new live microbes into the mix. Fermented foods such as kombucha and kefir can also be helpful to add more microbial diversity to your gut microbiome.
BUT—what are the best foods for me right now?
Eating a wide variety of healthy superfoods, like those mentioned above, to support a happy and healthy gut is a great place to start.
But, what if those foods that nutritionists and doctors all tout as being “superfoods,” aren’t healthy for YOU? Everyone’s body and body’s response to foods is different. Why is that? Because the makeup of microbes in your gut microbiome is completely unique to you. From the time you were born your microbiome has been shaped uniquely by things like location, whether or not you had a vaginal birth, what you ate as a child, what you’ve eaten throughout your life, antibiotics, life stress, and so much more. Since none of our health histories look exactly the same, it is impossible for us to all be able to consume the same kinds of foods without a problem.
Depending on your microbiome composition, you may react completely differently to broccoli and kefir than your best friend, your mother, or even your twin (if you have one)! While spinach is a favorite of your brother and gives him vitamin C and beta carotene, it may, in your gut, give your microbes fuel to create substances that are harmful.
The emphasis on these individual reactions to foods is important. It can make the difference between that healthy, rich and diverse microbiome that is working optimally and allowing your innate immunity to fight off infections, and a gut that is operating with a certain level of inflammation, with your immune response occupied so that fighting off the next cold could be harder.
References:
(1) Vyas U, Ranganathan N. Probiotics, prebiotics, and synbiotics: gut and beyond. Gastroenterology Research and Practice. 2012;2012:872716. doi:10.1155/2012/872716 PMID:23049548
(2) Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003;361(9356):512-519. doi:10.1016/S0140-6736(03)12489-0
(3) Patterson AG, Jackson SA, Taylor C, Evans GB, Salmond GPC, Przybilski R, Staals RHJ, Fineran PC. Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems. Molecular Cell. 2016 Dec 15;64(6):1102–1108. doi:10.1016/j.molcel.2016.11.012. PMCID: PMC5179492.
(4) Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, Iwasaki A. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5354–5359. doi:10.1073/pnas.1019378108. PMCID: PMC3069176.
