Microbiota differences might shape responses to viral infections

15.06.2026

New study suggests that modifying the gut microbiota could shape baseline immune states to improve infection resistance and responses to vaccines and immunotherapies.

What is already known

The immune system influences disease risk and responses to vaccines, cancer immunotherapy, and autoimmune treatments. Environmental factors—especially gut microbes—often shape immunity more than genetics, especially in animal models. But how microbiota differences influence immune activity in healthy people remains unclear.

What this research adds

Researchers analyzed blood and stool samples from 110 healthy adults and identified two major patterns of immune variation. One pattern was linked to the microbiota and showed higher baseline antiviral immune activity, increased numbers of specific immune cells, and lower inflammatory activity. This immune state was associated with microbial metabolic pathways that produce immune-modulating molecules, and both the immune and microbiota features were stable over time.

Conclusions

The findings suggest that modifying the gut microbiota could shape baseline immune states to improve infection resistance and responses to vaccines and immunotherapies.

The immune system influences disease risk and responses to vaccines, cancer immunotherapy, and autoimmune treatments. Now, a small study in humans shows that differences in people’s gut microbiotas are linked to variation in their baseline immune activity—especially antiviral responses.

The findings, published in Cell, suggest that modifying the gut microbiota could shape baseline immune states to improve infection resistance and responses to vaccines and immunotherapies.

Environmental factors—especially gut microbes—are known to shape immunity more than genetics, especially in animal models. But how microbiota differences influence immune activity in healthy people remains unclear.

Joel Babdor at the University of California, San Francisco, and his colleagues studied 110 healthy adults to understand how differences in the immune system and gut microbiota are connected.

Antiviral activity

The researchers collected blood, stool samples, and health surveys from the study participants, then analyzed immune cells, gut microbes, and their metabolites. Even though all participants were healthy, there were differences between individuals in both immune cell types and gut bacteria composition. Differences in certain immune activities—especially baseline antiviral immune activity and inflammation responses—were linked to differences in the gut microbiota and microbial products, the researchers found.

One of the major patterns linking the immune system and the gut microbiota reflected differences in how strongly people’s bodies activate interferon responses, an important part of antiviral defense. People with a higher baseline antiviral immune activity showed stronger activity of interferon-related genes and had higher levels of interferon-related signaling molecules in their blood.

These same patterns have been associated with people who respond better to influenza vaccines and with people with cancer who benefit from certain immunotherapies, the authors say.

Immune responses

People with patterns linked to stronger antiviral immune activity also had more specialized immune cells, and these immune traits were linked to gut microbes that produce beneficial molecules such as short-chain fatty acids. Both the immune and microbiota features were stable over time, the researchers found.

Although the study involved a small group of people and the clinical significance of the identified patterns remains unclear, the findings may explain why people differ in disease risk and responses to vaccines or immunotherapies, the authors say.

“We envision that the data resource presented here will provide insights and context for efforts to modulate the microbiome and the immune system for therapeutic benefit through approaches including dietary interventions, microbial colonization, or microbiome-informed precision immunotherapy,” they say.