How Altitude and Air Travel Disrupt the Gut—and What to Do About It

Jul 30, 2025 - 09:56

Updated: 9 months ago

How Altitude and Air Travel Disrupt the Gut—and What to Do About It

A headache after hiking in the mountains and a bit of digestive discomfort after a flight could be caused by the same mechanism—the microbes living in your gut.

The change in oxygen level as you move to higher altitudes can shift gastrointestinal (GI) microbial communities, including which bacteria are dominant and overall diversity. This shift can impact the health and function of cells in your intestinal lining—leading to symptoms like fatigue, bloating, gas, diarrhea, constipation, and nausea.

Those who frequently fly and travel to high altitudes are particularly affected. It’s such a problematic phenomenon that registered dietitian Jill Mongene has specialized in helping pilots, calling herself the “aviator dietitian.”

Anytime the body remains at an altitude above what it’s used to, problems can arise. Sometimes an altitude change can bring on symptoms that indicate bigger, underlying issues, she told The Epoch Times.

“They’re telling us everything starts in the gut, and that’s true. It affects our immune system, our mental status, our blood pressure, our blood sugar,” Mongene said. “People with really good gut health seem to function really well with flying, and those who don’t have a really hard time.”

Even short periods in higher altitudes—whether in aircraft or on mountains—can affect overall health. You can become acutely sick, and there’s also a risk of repeated altitude changes associated with chronic conditions such as irritable bowel syndrome, heartburn, indigestion, and constipation. Yet evidence shows your body can adapt and even thrive in higher altitudes.

Effects of Altitude

High altitude triggers the release of inflammatory cytokines, signaling proteins that tell the body to mount a defense against a threat like an infection or stress. Low atmospheric pressure puts stress on the body in the form of hypobaric hypoxia, a condition in which less oxygen is available with each breath. Hypoxia lowers oxygen in body tissue and affects the brain, including altered judgment.

While normally a healthy part of the immune system, cytokines can accumulate at too high a level in some cases.

In the case of altitude, too many cytokines can contribute to the development of acute mountain sickness, which causes headaches, fatigue, and the inability to sleep. It can affect climbers, hikers, and skiers typically at 8,000 feet or higher and may warrant medical attention. In rare, serious cases, high-altitude pulmonary edema and high-altitude cerebral edema can occur above 10,000 feet.

Further, some medications used for altitude-related illnesses, such as non-steroidal anti-inflammatories, may worsen gastrointestinal symptoms and cause GI bleeding.

Exertion—exercise during or after an altitude change—or climbing to a high altitude too fast or going too high can contribute to risk.

Other factors that might explain why some people are more susceptible to the effects of altitude are genes, overall health, inflammatory conditions before or after travel, and your microbiome, which can affect cytokine production and how your body reacts to hypoxia.

Microbiota and Hypoxia

The gut microbiome explains, at least in part, why some people acclimate more readily to higher altitudes when traveling.

Researchers sent healthy Chinese men living in a lowland plain to travel to the Qinghai–Tibet Plateau to determine how their gut microbiomes reacted to high altitude. The microbes in their stool samples were studied throughout the 108-day study and compared to those of men living in a high-altitude setting.

The traveling men stayed in the Qinghai–Tibet Plateau for 73 days, then nearly half returned to the lowland area.

“The results indicated that short-term hypoxia significantly altered the gut microbiota composition, especially in the early exposure stage. This change was primarily modulated by the increased abundance of Blautia A species,” the authors of the study, published in Genome Biology, wrote.

An eventual microbial shift to more Blautia A species offered a protective effect. The researchers went on to confirm the findings with additional animal experiments that verified Blautia A species play a role in butyric acid production.

Butyric acid, sometimes called butyrate, is a short-chain fatty acid beneficial to the gut’s ecosystem. It feeds cells lining the colon, essentially preventing leaky gut by promoting a healthy gut barrier.

Leaky gut is a condition in which bacteria and various molecules cross into the blood and brain, causing inflammation. Though leaky gut is not yet a clinical diagnosis, it has been been confirmed in some instances of irritable bowel syndrome and indigestion and may explain why some people who frequently fly have ongoing GI issues.

Increasing Butyrate

The authors noted that their findings could lead to the development of Blautia probiotic supplements to improve butyrate production. However, a quick-fix solution might not be straightforward. Butyrate supplements already abound on the market, with little evidence of benefit.

Butyrate, when given therapeutically in cases of metabolic disease, has shown limited benefits, according to Dr. Chris Damman, a gastroenterologist at the University of Washington School of Medicine, who studies how nutrition affects health via the microbiome.

On the other hand, eating the right foods to generate short-chain fatty acids is most beneficial to protect against a wide variety of symptoms, he said in a news release.

Butyrate is produced when we eat high-fiber foods.

“Then you get butyrate at the right time, in the right place, and in the right amounts,” Damman said.

Improve Diet Slowly

It might be tempting to rapidly increase fiber intake—especially in advance of a flight. However, Mongene said it’s best to start slowly. Eating high-fiber foods gradually will help build up good bacteria that produce butyrate. Changing the diet too quickly can lead to uncomfortable symptoms such as gas and bloating.

She suggested starting with a half-cup of beans and waiting at least a day for potential reactions. If you tolerate that, she said to begin slowly increasing fiber intake.

The federal government recommends about 28 grams of fiber daily as part of a 2,000-calorie diet, though most Americans fall far short of this goal. You’d have to eat two cups of pinto beans to reach 28 grams, though experts recommend getting fiber from diverse sources.

Sources easy-to-digest fiber include oatmeal, bread, pasta, and rice, Mongene said and could be better choices for those worried about being gassy on flights. However, whole fruits, vegetables, legumes, and nuts are better for feeding good bacteria.

You can also increase the good bacteria in your gut through fermented foods such as sauerkraut, pickles, yogurt, and hard cheeses. Mongene said to start slow on these foods, too, if you’re not accustomed to eating them.

Other Modifications

Simple lifestyle changes have helped Mongene’s pilot clients resolve GI-related issues, including:

Reduce saturated fats, which are mostly found in animal products, by eating more fish, poultry, and plant-based fats like nuts, seeds, edamame, olives, and avocado. Avoid high-fat ground beef and choose more lean cuts of beef.
Consider testing and supplementing for vitamin D3, B12, and omega-3 deficiencies.
Don’t drink alcohol or use drugs before or during travel.
Don’t fly if you’re sick.
Improve hydration and take electrolytes, especially when traveling.

Hydration is a major issue for Mongene, particularly when it comes to getting electrolytes, such as sodium, which are crucial for the body to operate optimally. Inadequate water intake decreases immune cells and causes changes in gut microbial composition, making the body more vulnerable to infections.

Mongene said dehydration can also mimic other health conditions, such as high blood pressure and high blood sugar, which is problematic for people who have diabetes.

“For every hour you’re flying, the more fluid you’re losing,” Mongene said. “The dehydration factor often shuts the gut down.”

Implications for Overall Wellness

The relationship between altitude, hypoxia, and the gut microbiome can further understanding of many diseases associated with hypoxia, including lung diseases such as chronic obstructive pulmonary disease and asthma, illnesses like COVID-19, and obstructive sleep apnea.

Hypoxia can cause irreversible damage to the body, and evidence shows that the intestine plays a critical role in the condition. It can sneak up on anyone, especially endurance athletes, climbers, and pilots.

Everyone reacts differently to hypoxia, and pilots undergo special training to know their own physiological cues.

Symptoms of hypoxia include increased breathing, lightheadedness, tingly or warm sensations, sweating, tunnel vision, dizziness, and euphoria. It can be hard to identify, according to a Federal Aviation Administration brochure.

“Unfortunately, our body doesn’t give us reliable signals at the onset of hypoxia—oxygen starvation—unless we have received special training to recognize the symptoms,” the brochure states. “In fact, it’s quite the contrary. The brain is the first part of the body to reflect a diminished oxygen supply, and the evidence of that is usually a loss of judgment.”