How Your Gut Health Affects Your Long COVID Risk

You might not think your gut health has much to do with COVID-19. While some people may experience gastrointestinal (GI) upset as a symptom of acute COVID-19 infection, diarrhea and vomiting are relatively uncommon compared to fever and cough.

Still, research has shown that the virus that causes COVID-19 lingers in the gut long after it leaves the lungs. One study published in 2022 found that a small portion of patients—around 13%—continued to shed the virus in their feces for four months or more after infection. An even smaller group had evidence of virus in the gut seven months after infection.

The movement of the virus through the gut has enabled epidemiologists to track COVID-19 in wastewater samples and has raised questions about how gut health may be involved in long COVID. 

More research is needed to understand better why some people infected with COVID-19 recover quickly while others suffer long-term symptoms. Because the virus is still relatively new and COVID-19 symptoms can vary greatly, expert virologists are unsure what makes some people susceptible to long-term effects—but one theory suggests it has to do with the gut.

COVID Infection Affects Diversity in the Gut Microbiome

The microbiome refers to the communities of bacteria, viruses, and fungi in the gut, gastroenterologist Christopher Vélez, MD, told Verywell in an email. These microbiota work together harmoniously to support various bodily processes, including:

• Metabolism
• Nutrition
• Physiology
• Immune function

Factors including diet, certain medications, and illness can impact the balance of good and bad bacteria in your gut. COVID-19 is one such illness that may disrupt your gut microbiome, especially in severe cases requiring antibiotics and hospitalization.

Given the presence of the coronavirus in the digestive tract long after initial exposure and infection, researchers are exploring a potential connection between the gut microbiome and long COVID.

In studies since 2020, researchers have observed a significant reduction in gut and lung microbiome diversity in people with COVID-19. According to a review published in March 2023, this loss of diversity was more pronounced on the gut level, and it was noticeable from the early stages of COVID-19 infection onward.

However, existing research does not show whether gut dysbiosis associated with COVID-19 resolves after the body clears the infection or if it persists in some people. If the imbalance in the gut continues after the infection, it’s possible that it could contribute to long COVID symptoms via the gut-brain and gut-lung axis.

Understanding the Gut-Brain Axis

The gut and the brain are intertwined via the gut-brain axis, a communication network of nerves, neurotransmitters, and gut microbes implicated in digestive disorders. The gut is sometimes referred to as a “second brain” because so many nerves are embedded in the intestinal lining.

Recent research suggests that the gut-brain axis can influence inflammation, mood disorders, and the immune and endocrine systems. It remains to be seen whether the same pathway is involved in long COVID.

Vélez, a gastroenterologist in the Center for Neurointestinal Health of Massachusetts General Hospital, said chronic GI distress after COVID-19 is likely linked to the gut-brain axis. He has worked on multiple studies of people recovering from COVID-19, including ones that specifically considered long-term GI symptoms.

In a study of post-COVID GI symptoms (i.e., diarrhea, vomiting, or stomach pain), Vélez and colleagues found that people assigned female at birth and those with a history of depression or anxiety both had a higher risk of developing a new GI disorder after COVID infection. The presence of GI symptoms during an initial COVID-19 infection did not seem to be associated with a higher risk of long-term GI symptoms.

Irritable bowel syndrome (IBS) is considered a disorder of the gut-brain axis because it’s usually characterized by digestive distress in the absence of pathology in the gut. Another study used the Rome IV criteria for diagnosing IBS and found that people recovering from COVID-19 had significantly higher rates of new IBS than those who did not have COVID.

While researchers theorize that post-COVID gastrointestinal disorders stem from the gut-brain connection, further research is needed to confirm this suspicion and direct therapies, Vélez said.  

Gut Health May Be a Factor in COVID Recovery

The makeup of your microbiome may also influence your recovery from COVID-19 infections. Vélez said a common medical doctrine is “sicker people get sicker”—a bit of a generalization, but not far from the truth.

“Those who have better overall health (including the GI tract) have a better chance of an acute COVID-19 recovery,” Vélez said. “This is the case [for] many infections like pneumonia. What this means for long COVID is unclear.”

A small study of people with COVID-19 in Norway revealed that those who required intensive care unit (ICU) admission during hospitalization had lower diversity in their microbiomes compared to those who were hospitalized but did not require intensive care. This association held up when researchers factored out other predictors of disease severity, such as medication use and chronic lung disease.

People prone to severe COVID-19 complications—including older adults and people with underlying conditions such as heart disease, diabetes, and asthma—also tend to exhibit reduced microbiome diversity. A team at Houston Methodist is currently investigating this association to find out if altered microbiome diversity triggers prolonged inflammation in people with COVID-19 and whether this is a clue to understanding long COVID.

Probiotics Are Not Recommended for Treating COVID Symptoms

With more research, it’s possible that scientists could identify gut microbiome signatures associated with long COVID and use that information to recommend therapies such as probiotics. But the research isn’t there yet, Vélez cautioned.

“The data is a bit spotty,” Vélez said. “My approach to pro- and prebiotics is that the types of diets and lifestyles associated with overall health—more vegetables, more fruit, less processed food, less meat, [more] physical activity—likely do more good for you.”

If you are inclined to use probiotic supplements to help your gut heal from COVID-19, be aware that supplements are not regulated like medications in the United States. Vélez recommends talking to a primary care provider before you go out and buy probiotics.

“I certainly would not spend a lot of money on them, but you can try them,” he said.