Microscopic view of viruses and bacteria in the gut.

Gut Check: How Antibiotics Impact Your Viral Defense Team

Nico Varela in Health & Wellness December 2025 • 4 min read.

"A new study uncovers the surprising effects of long-term antibiotic use on the delicate balance of viruses in your gut and mouth – and what it means for your health."

Our bodies are complex ecosystems, teeming with trillions of microorganisms. Bacteria often steal the spotlight, but viruses also play crucial roles in maintaining this delicate balance. These viral communities, known as viromes, are integral to our health, influencing everything from our immune response to our susceptibility to disease.

Antibiotics, while vital for fighting bacterial infections, can inadvertently disrupt this carefully constructed microbial landscape. When we take these medications, they not only target harmful bacteria but also affect the beneficial ones, potentially altering the composition and function of our viromes. But what exactly happens to these viral communities during antibiotic use, and what are the long-term consequences for our health?

A groundbreaking study sheds light on this critical question, exploring how long-term antibiotic therapy impacts the viral communities in the human gut and mouth. The findings reveal surprising differences in how these two body sites respond to antibiotic use, offering new insights into the complex interplay between bacteria, viruses, and our overall well-being.

The Oral-Gut Divide: How Antibiotics Reshape Your Virome

Microscopic view of viruses and bacteria in the gut.

Researchers at the University of California, San Diego, delved into the effects of long-term antibiotic therapy on the oral and fecal viral communities of human subjects. The study revealed that while both body sites experienced changes in their viral composition, the nature and extent of these changes varied significantly.

The study design included collecting saliva and fecal samples from participants undergoing a six-week course of intravenous antibiotics. These samples were analyzed to identify and quantify the different types of viruses present, providing a snapshot of how the viral communities evolved over time. Key findings included:

Distinct Viral Communities: The viral communities in the mouth and gut differed significantly, with the gut exhibiting a more diverse range of viruses compared to the mouth.
Oral Viromes More Diverse: Surprisingly, the oral viromes showed greater overall diversity than those in the gut, suggesting different ecological pressures in these two environments.
Papillomavirus Increase in the Mouth: Subjects on antibiotics showed an increased abundance of papillomaviruses in their mouths, hinting at a potential link between antibiotic use and viral activity.
Antibiotic Resistance Genes Rise in the Gut: The gut viromes of individuals on antibiotics displayed a notable expansion of genes associated with antibiotic resistance, a phenomenon not observed in the oral viromes.

These findings underscore the complex and site-specific ways in which antibiotics can reshape our viral ecosystems. While antibiotics didn't significantly impact overall viral diversity, the expansion of antibiotic resistance genes in the gut viromes raises important concerns about the potential for viruses to contribute to the spread of antibiotic resistance.

Protecting Your Virome: What You Can Do

While the study highlights the potential for antibiotics to alter our viral landscape, it also underscores the importance of understanding and protecting our microbial ecosystems. By making informed choices about antibiotic use and adopting strategies to support a healthy gut, we can help safeguard our viral defense team and promote long-term well-being.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

Everything You Need To Know

What are viromes and why are they important for health?

Viromes are viral communities that exist within our bodies, including the gut and mouth. They are composed of various viruses that play crucial roles in maintaining the delicate balance of our internal ecosystems. These communities influence our immune response and susceptibility to disease. Understanding the virome is crucial because its composition and function impact overall health and well-being. Changes in the virome, such as those caused by antibiotics, can have far-reaching consequences, affecting how our bodies function and respond to various challenges.

How do antibiotics affect the viral communities in the gut and mouth?

Antibiotics, while designed to fight bacterial infections, can significantly disrupt the viromes in both the gut and the mouth. A recent study showed that the effects of antibiotics are site-specific. While the overall viral diversity may not be significantly impacted, there are notable changes. In the mouth, the use of antibiotics can lead to an increase in papillomaviruses. In the gut, antibiotic use can lead to an expansion of genes associated with antibiotic resistance within the virome. This highlights the complex and varying ways antibiotics can reshape the viral landscape in different parts of the body.

What were the key findings regarding the oral and gut viromes in the study?

The study comparing the oral and fecal viral communities revealed several key findings. Firstly, the viral communities in the mouth and gut differed significantly, with the gut exhibiting a more diverse range of viruses. Secondly, the oral viromes showed greater overall diversity than those in the gut, indicating different ecological pressures in these two environments. Thirdly, subjects on antibiotics showed an increased abundance of papillomaviruses in their mouths. Lastly, the gut viromes of individuals on antibiotics displayed a notable expansion of genes associated with antibiotic resistance, a phenomenon not observed in the oral viromes.

Why is the expansion of antibiotic resistance genes in the gut virome concerning?

The expansion of genes associated with antibiotic resistance in the gut virome is concerning because it suggests a potential for viruses to contribute to the spread of antibiotic resistance. Viruses, by carrying these resistance genes, can potentially transfer them to bacteria, making the bacteria resistant to antibiotics. This can reduce the effectiveness of antibiotics in treating infections, posing a significant challenge to public health. It highlights the intricate relationships between bacteria, viruses, and antibiotics within our bodies, emphasizing the need for careful antibiotic use and strategies to support a healthy gut.

How can one protect their virome in the face of antibiotic use?

Protecting the virome involves making informed choices about antibiotic use and adopting strategies to support a healthy gut. Antibiotics should be used only when necessary and as prescribed by a healthcare professional. Proactive steps include consuming a balanced diet and considering the use of probiotics. These measures can help maintain a healthy balance of microorganisms, including viruses, and support the overall health of the gut and other ecosystems within the body. Understanding the impact of antibiotics on the virome encourages responsible antibiotic use and a focus on gut health to safeguard our viral defense team.