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BackTable / ENT / Article
Factors That Shape Your Microbiome & Sinus Health: Diet, Environment & Probiotics
Iman Iqbal • Updated Jul 31, 2025 • 37 hits
As awareness grows around how lifestyle and exposure can affect overall health, patients and providers alike are beginning to question long-held assumptions about common sinus conditions, allergic rhinitis, and the role of the microbiome in upper airway disease. Recent scientific advances are changing the approach to managing chronic nasal symptoms and allergies.
Drawing on the expertise of Dr. Jennifer Villwock, an otolaryngologist, this article explores how standard treatments may fall short and how incorporating new insights into the microbiome, immune modulation, and patient-centered care can improve outcomes. From everyday dietary choices to innovative therapies, adopting a more personalized and integrative approach to sinus health can enhance symptom control and overall well-being.
This article features excerpts from the BackTable ENT Podcast. We’ve provided the highlight reel in this article, and you can listen to the full podcast below.
The BackTable ENT Brief
• Though many report improvement after cutting out foods like dairy or gluten, scientific evidence linking diet to chronic nasal issues is still limited. True IgE allergies are uncommon; most cases involve sensitivities or low-grade inflammation.
• Popular food intolerance tests like IgG panels or hair analysis lack scientific support. The elimination diet remains the most practical approach to identifying food triggers.
• Air pollution, particularly fine particulate matter (PM2.5), can provoke inflammation, bypass nasal defenses, and even affect long-term cardiovascular and cognitive health.
• Concerns about overuse of nasal steroids in children are leading some families to seek earlier use of immunotherapy as a safer long-term option.
• Dysbiosis, or microbial imbalance, is an emerging factor in treatment decisions for chronic sinus or allergy patients, influencing choices like topical treatments and antibiotics.
• While evidence for nasal probiotics is still evolving, oral probiotics, via supplements or fermented foods, are often used to protect gut health during antibiotic therapy and may offer immune support.
• For those seeking evidence-based understanding, review articles, PubMed searches, and recent studies offer deeper insight into the microbiome’s role in sinonasal health.
• Intralymphatic immunotherapy, delivering allergens directly to lymph nodes, may offer faster results than traditional desensitization, but larger trials are needed to confirm its benefits and effects on the microbiome.
Table of Contents
(1) How Diet & Environment Affect Sinus Health
(2) Chronic Sinus Treatment Beyond Antibiotics
(3) The Future of Immunotherapy, Probiotics & Sinus Microbiome Research
How Diet & Environment Affect Sinus Health
With growing awareness of the connection between lifestyle and immune health, many patients, especially parents, are asking whether dietary changes can help manage chronic nasal conditions like congestion and allergic rhinitis. While some children seem to improve after cutting out dairy, gluten, or processed foods, the scientific link between food and sinonasal symptoms is still not fully established. Most of these improvements are anecdotal, and true IgE-mediated food allergies are relatively rare. More often, symptoms are due to intolerances, food additives, or chronic low-grade inflammation, which are harder to measure. Although tests like IgG food panels and hair analyses are widely marketed, they are not scientifically validated. Instead, elimination diets, though difficult to follow, remain the most practical way to identify food triggers.
Environmental exposures are another important factor in allergy development and overall immune health. Fine particulate matter (PM2.5) in polluted air can bypass the nasal filtering system and deposit in the lungs, triggering inflammation and contributing to long-term risks like cardiovascular disease and cognitive decline. There's also growing concern about overusing medications like nasal steroids in children, which may impact growth or immune function. This has led some parents to consider immunotherapy earlier in treatment. Looking ahead, better understanding of the sinus microbiome could lead to new therapies like targeted nasal probiotics or rinses that support beneficial bacteria and reduce inflammation.
[Dr. Ashley Agan]
If we think of different external factors that affect our gut health, I immediately think of dietary factors. We think of, especially with allergy, food allergy, I guess, per se, which definitely is not my realm, but people will ask, especially if they're bringing their kid in for chronic congestion, runny nose, should I cut dairy out? Should we try not doing gluten? Should we not try-- Do you feel that some of the dietary changes affect potentially whether it's the gut, the microbiome, I don't know if this is a little bit too naïve, the microbiome in general for our bodies, or specifically sinus microbiome, if it affects the gut that then affects the sinus, do you think those modifications work in that mechanism, I guess, or do we just not know yet?
[Dr. Jennifer Villwock]
I think that conversation can become very complicated because there's true IgE-mediated food allergy, which should have very clear, very reproducible symptoms. Then you also have the lactose intolerances of the world, which is not an IgE-mediated phenomenon. Then you can add another layer of complexity onto that because now there's all sorts of food additives and other things, which some people can be sensitive to as well. If you're interested in that topic, come to the AAOA Course in Vail. There will be some sessions on that are related to food-related sensitivities and additive sensitivities.
I think it becomes very complicated. A lot of times people will say, "Well, I looked online and I can order this test that's going to tell me if I'm allergic to all these different foods." Historically, a lot of those tests have not been super clinically helpful because there's a difference between a reaction that can be precipitated in a lab versus actually having that clinically relevant reaction to that. What I counsel patients on is that, "Well, if you're concerned about this particular food or food group giving you symptoms, the best way to figure that out is just to go on an elimination diet, then you can slowly add these things back in and see if there's a change in the symptoms."
Having tried an elimination diet in the past, it is super unpleasant and very difficult. I think it's a special patient who is so motivated that they're going to say like, "Yes, I'm going to eliminate corn, soy, wheat, gluten." There are so many things if you want to do it thoroughly that I think it can be a real challenge for folks. The flip side of that for your patient who's a child who has the sniffles, a lot of parents I think are really concerned about some of the side effects of our first line medications. Depending on where you buy your little thing of fluticasone, it's either going to say, do not use this for more than two months.
It's going to say, ask your doctor if this needs to be used for more than two months. I think that's another opportunity to have a conversation about, well, in children who are sensitized and allergic to many things, we know that early initiation of immunotherapy can help with a number of things. First, your allergen specific reactions that you're having now, it can prevent future sensitizations and it can prevent things like progression to asthma and asthma severity. I think it behooves you to have, even if you don't offer immunotherapy or allergy testing in your office, I think it behooves you to have that skillset in your mind so that you're not just playing this whack-a-mole, okay, we'll do Flonase for two weeks or two months and then they get better, but the label says to stop. Then they stop and now they're worse, and that's not really optimizing the health of that child at all.
[Dr. Ashley Agan]
Yes, no, that's a really good point. When I think diet is obviously frequently talked about when it comes to microbiome and it makes sense, because it's like we put things in our mouth and they're going down into our stomach and then bacteria are eating up some of it too or whatnot. What about other non-diet types of things affecting our microbiome, whether it be in our gut or in our nose or elsewhere? Things like exercise, environmental exposure, air quality, pollution, are those playing a role?
[Dr. Jennifer Villwock]
Yes, I think the data for those, I think is much more robust in, for example, the airway literature. There's a lot of studies on things like PM 2.5, which is particulate matter. The reason there's so much focus on 2.5 is because it's small enough that it's going to bypass our nose and sinuses and get right into the lower lung, lower airway. There's a lot of robust literature that's emerging about the impacts of particulates of that size and how they relate to cardiovascular health, pulmonary health, even factors like dementia. Certainly, there's tons of stuff floating around that we're breathing in allergies and irritant-wise. I think that most of the literature shows that a lot of those things are going to contribute to more of that pro-inflammatory state.
[Dr. Ashley Agan]
Do you think we'll ever get to the point where some of like we understand the microbiome enough in a patient to where now we're not just like, immunotherapy to modulate your immune system for sensitivity, but, oh, we're going to also have treatment parameters or tools potentially to get your microbiome back healthy and your sinuses? Do things like, and this might sound even more naïve or silly, but, do basic sinus rinses help us get our microbiome in check? Will we have something as basic and as broad as sinus rinses to something more specific where it's topical probiotics, for example, certain dosages or treatment parameters that can help us modulate somebody's sinus microbiome?
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Chronic Sinus Treatment Beyond Antibiotics
As more patients present with chronic sinus or allergy conditions that don’t fully respond to standard treatments, clinicians are turning to a broader understanding of disease, one that includes the nasal microbiome. Although microbiome research is still emerging, disruptions in microbial balance (dysbiosis) are increasingly considered when deciding whether to continue or adjust therapies. Instead of reflexively prescribing another round of oral antibiotics, providers may now weigh alternative options like topical treatments, frequent debridement, or long-term approaches such as immunotherapy. These decisions rely heavily on shared decision-making, especially when clear clinical guidance is lacking.
There’s also renewed interest in supporting microbial health through probiotics. While research on topical sinus probiotics has slowed, oral probiotics remain popular for their low risk and potential systemic benefits. Some clinicians routinely recommend probiotics, either as supplements or through fermented foods, when prescribing antibiotics, with the goal of protecting gut health and possibly supporting immune balance. Though the direct impact of probiotics on nasal microbiota remains unclear, incorporating them reflects a growing trend toward more holistic, microbiome-aware allergy and sinus care.
[Dr. Ashley Agan]
When you think about dysbiosis, maybe whether it be like in the nasal microbiome or the gut or what have you, is that part of your clinical decision-making? When you have the patient in front of you and let's say, you talked earlier about how you're at the end of the road and you've done all the things, you've reached in your toolbox and you're like, we do this, we do this, we do this. How do you think about it when the patient is in front of you? Are you culturing the inside of the nose? Has the research made it to the bedside or is it still mostly in papers right now?
[Dr. Jennifer Villwock]
I think a lot of it still remains in the realm of papers. It's certainly something that I think about because I think we'd be doing ourselves a disservice not to think about it, at least to keep it in our mind. Like do I really want to put this person on like their fifth oral antibiotic course, type thing. I think this is where it becomes really important to have shared decision-making conversations with your patients. As you guys already know about me, I'm an over-explainer. I go into all these rabbit holes. I present people way more information than perhaps is helpful for them, but I want them to understand my thought process.
I absolutely have these conversations with folks about, well, for a lot of these situations, we're in a state of equipoise in terms of we have these different options. There's not clearly one that's superior to another, because if there was, obviously I would offer you the superior one, and these are all the things to consider. That's a conversation about, well, do we do another round of oral antibiotics? Do we just bring you in for more frequent debridement's? Do we do topical antibiotics? do we want to do allergy testing not to satisfy your curiosity, because just knowing what you're sensitized to is not helpful, but to potentially then pursue that three to five-year treatment course to see if this can get you some added benefits.
One area that I hope will experience a renaissance is investigations into topical probiotics for the sinuses, which was a hot topic maybe 10 years ago or so and has nosedived, but personally, I would love to see a resurgence in the research in that realm, because I think that it's an area that's really needed.
[Dr. Ashley Agan]
I do remember conferences several years back where this was a little bit, the whole microbiome was hot, fresh, and in front. Then I remember patients asking, well, and usually patients will ask, should I take a probiotic if we're going to do whatever antibiotic? Should I be taking a probiotic regularly because I have all these infections? What are your thoughts on oral probiotics for sinus disease or allergy symptoms?
[Dr. Jennifer Villwock]
In general, I would say they're in that category of unlikely to harm, may help. I do make it part of my standard practice with patients to anytime I'm prescribing an oral antibiotic, I also counsel them about not just some of the topical probiotic pills and things that you can get, but also foods that you can eat that are naturally fermented. They're going to have a probiotic mix within them and to increase their consumption for all the reasons that we talked about. Do I think that it is plausible that oral probiotics that impact gut health may at the same time be impacting our microbiome elsewhere?
I think it's definitely possible. I think that that's something that hasn't been studied, but I would put it in the realm of possible. If patients are getting additional benefit from that, then I think that's great. I don't know how I would tease that out in a clinical context, but I think certainly for gut microbiome protection, I do talk to patients about that for sure.
The Future of Immunotherapy, Probiotics & Sinus Microbiome Research
Clinicians and researchers continue to explore the evolving landscape of the nasal microbiome and its role in allergy and sinus disease. For those looking to deepen their understanding, modern literature searches on platforms like PubMed and Google Scholar can yield valuable insights. Keywords such as sinusitis, nasal microbiome, immunotherapy, and probiotics are useful starting points. As interest in this space grows, recent studies have focused on the potential benefits of immunotherapy in modifying the nasal microbiome, especially in patients with allergic rhinitis and nasal polyps. However, the field still relies heavily on small-scale studies, limiting broad clinical application at this stage.
Looking ahead, new techniques such as intralymphatic immunotherapy are generating interest as a potentially more efficient and targeted approach. This method involves injecting allergens directly into lymph nodes, particularly the inguinal nodes, to induce immune tolerance. Early trials suggest that only a few well-timed injections may yield results comparable to traditional three-to-five-year regimens. However, the efficacy of this approach depends not only on the antigen itself but also on how it is delivered and recognized by the immune system. Further research is needed to define ideal patient populations, assess microbiome shifts, and measure immunologic markers like IL-10 following treatment. While this area holds promise, large-scale studies are essential before such strategies can be widely adopted in clinical care.
[Dr. Ashley Agan]
It makes sense. Going back to the sinus microbiome or for allergy testing, if our listeners wanted to learn more about the microbiome, immunotherapy, allergy treatment, do you have any studies or reading or podcasts that you recommend? Granted, for any of our listeners, you still have time to register for the Vail meeting, which sounds like it's going to be amazing because you're the program chair for it, the course director, which is awesome. Do you have any recommendations?
[Dr. Jennifer Villwock]
Literature searches are my love language. I have so many.
[Dr. Ashley Agan]
What keywords are you typing in? Are you using Wikipedia or ChatGPT ever for these as well?
[Dr. Jennifer Villwock]
Yes. I've had some instances where I have been very unimpressed with what ChatGPT has told me. I am primarily just using good old PubMed.gov and Google Scholar. If you put in keywords like sinusitis, microbiome, immunotherapy, nasal microbiome, you'll find all sorts of stuff that comes up. I'm trying to focus more on the more contemporaneous literature, you can filter down so that you're not getting 10,000 million different hits just by searching for within the past 5 to 10 years, particularly if you're interested in probiotics and those other things.
Those will pull up some of those papers that Gopi and I were talking about in terms of this being more of a hot topic 8 to 10 years ago. The other thing that is nice is as we're having so much more literature in this area, if you're doing your lit search, you can also click the box that says just show me reviews, because that'll give you a nice synthesis of everything that has already been published in hopefully a very digestible format.
[Dr. Gopi Shah]
I love a good review article.
[Dr. Ashley Agan]
Anything on the horizon to be on the lookout for? Do you think if you could gaze into your crystal ball, how do you think this is going to translate into clinical care 10 to 20 years from now?
[Dr. Gopi Shah]
Are you going to have beakers and vials of topical probiotics that you're going to be testing and producing?
[Dr. Jennifer Villwock]
I am hopeful that others, not necessarily me personally, will take up the mantle of how efficacious or not. Sometimes it's helpful just to know like these don't work, so let's stop revisiting it.
[Dr. Gopi Shah]
Cross it off.
[Dr. Jennifer Villwock]
Yes, but I think the topical probiotics is an interesting question. I think continuing to do studies on changes in the nasal microbiome after immunotherapy, whether it's subcutaneous or sublingual, in our allergic rhinitis as well as our nasal polyp and other patients will be very helpful. Most of the studies that have been done are relatively small. We do see signal in the noise in terms of, yes, there's differences in the bacterial compositions and things start to normalize with immunotherapy, but a lot of times those are limited to 40, 50, 60 patients. It's hard to really say this is valid for all the populations that we treat. Then on the horizon, there's a technique called intralymphatic immunotherapy. Have you guys heard of that one?
[Dr. Ashley Agan]
No.
[Dr. Jennifer Villwock]
The goal is to say, well, we know all this immunologic shenanigans that's happening in the lymph nodes, et cetera. Why don't we just give our immunotherapy to the lymph node? There are folks who are currently studying and there's been a number of clinical trials investigating, yes, what happens if we deliver our immunotherapy via targeted injection into inguinal lymph nodes? That circumvents some of the three to five-year treatment because a lot of times these protocols are just three-ish injections that are spaced out over a number of weeks and seeing, can we get the same immune tolerance effects?
I would be particularly interested in knowing who the ideal patient is for this. There's some issues in terms of, well, it's not as simple as just being like antigen into the lymph node. It matters like how it's packaged, what it's attached to, all of those things impact how your immune system is going to recognize that antigen. I think more information about the ideal way even to deliver intralymphatic immunotherapy and then, of course, really assessing symptoms, microbiome changes, IL-10 levels, et cetera after that treatment.
Podcast Contributors
Cite This Podcast
BackTable, LLC (Producer). (2025, February 25). Ep. 212 – Allergy Immunotherapy & The Microbiome [Audio podcast]. Retrieved from https://www.backtable.com
Disclaimer: The Materials available on BackTable.com are for informational and educational purposes only and are not a substitute for the professional judgment of a healthcare professional in diagnosing and treating patients. The opinions expressed by participants of the BackTable Podcast belong solely to the participants, and do not necessarily reflect the views of BackTable.
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