New Research: Cleaner Air Leads to Better Gut Health

We’ve long known that the air we breathe can shape our respiratory health—but new research is showing that indoor air pollution may also impact something deep inside our bodies: our gut microbiome and virome.¹

That’s right. A recent randomized controlled trial out of rural Uganda revealed something remarkable—when indoor air quality improved, not only did participants experience fewer breathing problems, but researchers also saw measurable changes in the gut’s microbial community. These findings are preliminary, based on a small sample size of 80 adult women, but they open the door to an exciting and important new area of study: how the gut and lungs may be connected in more ways than we ever imagined.

Graphic which states: “The gut microbiome and virome form a dynamic ecosystem that plays a vital role in overall well-being. New evidence shows this ecosystem is impacted by the air we breathe.”

What Is the Gut Microbiome—and What’s a Virome?

Before diving into the findings, let’s define a few key terms.

Your gut microbiome is the collection of trillions of microorganisms—mostly bacteria, but also fungi, protozoa, and other microbes—that live in your digestive tract. These microbes help digest food, produce vitamins, train your immune system, and even influence your mood and brain function.

A graphic synthesizing the information from the article about the microbiome, the trillions of microorganisms that live in your digestive tract, which assist with many biological functions and systems.

According to the Cleveland Clinic, a diverse, plant-rich diet is one of the most powerful ways to support a healthy gut microbiome.² Whole grains, fruits, and vegetables offer dietary fiber and micronutrients that not only nourish your body but also serve as fuel for beneficial gut bacteria. These foods help reduce inflammation and promote a stable, balanced microbial community. Overuse of antibiotics, on the other hand, can disrupt this balance, sometimes wiping out good bacteria and giving harmful ones room to grow.

The U.S. Department of Agriculture’s Agricultural Research Service (USDA ARS) explains that the gut microbial ecosystem thrives on components of our diet that human cells can’t digest—like resistant starches and certain types of fiber found in potatoes, beans, and oats.³These components are broken down in the colon by the microbiome, which uses its own specialized genetic toolkit to digest what our bodies cannot. This process not only supports beneficial bacteria but also increases microbial diversity—a key marker of health.

A graphic synthesizing the information from the article about the virome, all the viruses present in your gastrointestinal tract, which also help your body to function.

The gut virome, a lesser-known but equally important concept, refers to all the viruses present in your gastrointestinal tract. This includes viruses that infect bacteria (called bacteriophages), as well as viruses that may interact with human cells or other microbes. While we often associate viruses with illness, many in your virome actually help keep microbial communities balanced and healthy.

Together, your gut microbiome and virome form a dynamic ecosystem that plays a vital role in overall well-being. And now, there’s growing evidence that this ecosystem is impacted by more than just diet, stress, and antibiotics—it’s also influenced by the air you breathe.

The Study: From Kerosene Lamps to Solar Lights

Conducted by researchers at Harvard and Massachusetts General Hospital, the study looked at women in rural Uganda who were using kerosene lamps for indoor lighting—a major source of household air pollution. After receiving solar-powered lighting systems, participants were followed for 18 months.

Researchers collected stool samples, tracked respiratory symptoms, and conducted lung function tests before and after the intervention. The results?

Respiratory symptoms dropped significantly—from 57.1% to 36.1%.
There were clear changes in the structure and diversity of the gut microbiome and virome.
Women who showed these microbial shifts were also less likely to report breathing problems.
Interestingly, the virome showed even greater shifts than the bacterial microbiome after the air pollution exposure was reduced.

These results suggest that air pollution may harm lung health by first disrupting the gut’s microbial balance—a pathway referred to as the gut-lung axis.

Graphic reviewing the details from the article and the research: air pollution affects more than the lungs, the gut and lungs are connected, and cleaner air equals fewer symptoms.

The Gut-Lung Axis: A Two-Way Street

The gut-lung axis refers to the bidirectional communication between the gastrointestinal system and the lungs. In simple terms: what happens in your gut can influence inflammation and immune responses in your lungs, and vice versa. This is why gut health has been linked not just to digestion, but to respiratory conditions like asthma, COPD, and even lung infections.

This study is one of the first to provide experimental evidence—not just correlation—that air pollution can alter the gut microbiome, which may in turn influence lung health.

A graphic synthesizing the information from the article about the gut-lung axis showing what happens in your gut can influence your lungs, and vice versa.

Why This Matters

Although the sample size was small and the study focused on a very specific population, the implications are far-reaching.

Indoor air pollution is a global issue. Millions of people around the world still rely on kerosene, wood, or charcoal for light and cooking.
Gut health is increasingly recognized as central to wellness. This research adds air quality to the growing list of factors that shape the microbiome.
There’s potential for new therapeutic approaches. Could improving gut health help mitigate some of the harms caused by air pollution? Could gut microbes become biomarkers for air pollution exposure? These are questions worth exploring.

What You Can Do Right Now

While the science connecting air pollution and gut health is still emerging, one message is already clear: your daily choices matter. The state of your gut microbiome—and by extension, your immune function, mental clarity, and even resilience to disease—isn’t just shaped by your genetics. It’s shaped by your environment, your habits, and what you breathe, eat, and absorb every single day.

The good news? You don’t have to wait for more studies or any medications to start protecting yourself. There are practical, science-backed steps you can take right now to create a healthier home, support your body’s internal ecosystems, and reduce your risk of chronic inflammation and disease.

Support your microbiome—and virome:

Build a gut-friendly lifestyle by focusing on diversity in your diet. Choose fiber-rich whole foods like leafy greens, legumes, oats, and berries. These not only offer essential nutrients but also contain prebiotics—non-digestible fibers that feed beneficial bacteria. According to the USDA ARS, these fibers help good bacteria grow and may increase the diversity of your gut community, which is associated with better health outcomes.
Include probiotics, which are live microorganisms found in fermented foods like yogurt, kefir, kimchi, and sauerkraut—or in supplement form. These helpful microbes can re-balance your gut, especially after illness or antibiotic use.
The Cleveland Clinic recommends combining probiotics with prebiotics for a synergistic effect, known as synbiotics—where the food source (prebiotic) enhances the survival and activity of the beneficial microbe (probiotic).

Be careful with artificial sweeteners: While artificial sweeteners like sucralose and aspartame may negatively impact the gut microbiome, natural alternatives like stevia have shown potential to preserve or even increase microbial diversity, according to USDA ARS research.

Use antibiotics wisely: When necessary, they save lives. But overuse or misuse can wipe out beneficial bacteria along with harmful ones. Always consult your healthcare provider and avoid unnecessary prescriptions.

Invest in clean indoor air: Whether it’s through better ventilation, reducing sources of combustion, or using a high-quality air purifier like the Austin Air HealthMate, improving your indoor air quality can benefit both your lungs and your gut.

Final Thoughts

Cleaner air doesn’t just help you breathe easier—it may help your gut function better, too. While more research is needed, this small study is a powerful reminder of how deeply interconnected our bodies really are. The air we breathe, the food we eat, and the microbes within us are all part of one shared system.

As co-author Dr. Joseph Allen put it, this discovery “made in Uganda, is relevant news for everyone’s health.”⁴

REFERENCES

¹ Huang C, Nuwagira E, Tisza M, et al. (2025 May 21). Effect of household air pollution on the gut microbiome and virome of adult women living in Uganda. Environmental Health Perspectives. doi: 10.1289/ehp16002.

² Gut microbiome. (2025 May 9). Cleveland Clinic. https://my.clevelandclinic.org/health/body/25201-gut-microbiome.

³ Jiang, G. (2025 January 10). Keeping a healthy gut. USDA Agricultural Research Service. https://www.ars.usda.gov/oc/utm/keeping-a-healthy-gut/.

⁴ Feldscher, K. (2025 June 5). Cleaner indoor air helps breathing, alters gut microbiome—and suggests new ways to fight pollution harms. Harvard T.H. Chan School of Public Health. https://hsph.harvard.edu/news/cleaner-indoor-air-helps-breathing-alters-gut-microbiome-and-suggests-new-ways-to-fight-pollution-harms-study-finds/.