Surreal illustration of a disrupted microbiome.

Antibiotics and Your Microbiome: What You Need to Know

Lena Voss in Health & Wellness June 2025 • 4 min read.

"Discover the surprising long-term effects of antibiotics on your gut and oral health, and what you can do to protect your microbiome."

Our bodies are home to trillions of microorganisms, including bacteria, viruses, fungi, and archaea, collectively known as the microbiome. This complex ecosystem plays a crucial role in our overall health, influencing everything from digestion and immunity to mental well-being. Maintaining a balanced microbiome is essential for preventing disease and promoting optimal function.

Antibiotics, while life-saving in combating bacterial infections, can significantly disrupt this delicate balance. These medications don't discriminate between harmful and beneficial bacteria, often wiping out large portions of the microbiome. This disruption can have both short-term and long-term consequences, impacting our health in various ways.

Recent research has shed light on the specific effects of long-term antibiotic therapy on the human oral and fecal viromes – the viral component of the microbiome. Understanding these effects is crucial for making informed decisions about antibiotic use and taking proactive steps to protect our microbial health. This article will explore the key findings of this research and offer practical advice for supporting your microbiome.

How Do Antibiotics Impact Your Oral and Gut Viromes?

Surreal illustration of a disrupted microbiome.

A groundbreaking study published in PLOS One investigated the impact of long-term antibiotic therapy on the viral communities in the human mouth and gut. Researchers collected saliva and fecal samples from subjects undergoing a six-week course of intravenous antibiotics, comparing them to a control group that received no antibiotics. The study aimed to understand how antibiotics alter the viral landscape and whether these changes could contribute to antibiotic resistance.

The study revealed significant differences between the viral communities in the mouth and gut. The gut virome was found to be more diverse and heterogeneous than the oral virome, suggesting a more complex ecosystem. Key findings included:

Oral Virome Diversity: Antibiotics were associated with a surprising increase in papillomaviruses in the oral cavity, suggesting a potential link between antibiotic use and viral activity.
Fecal Virome Shifts: While antibiotics didn't significantly impact the overall diversity of the gut virome, they did lead to an expansion of genes associated with antibiotic resistance.
Bacterial Community Changes: The study also observed characteristic changes in the bacterial communities of the mouth and gut in response to antibiotics, further highlighting the interconnectedness of the microbiome.

These findings suggest that while antibiotics may not drastically alter the overall viral diversity, they can promote the development of antibiotic resistance in the gut virome. The increased presence of papillomaviruses in the oral cavity also raises questions about the potential long-term effects of antibiotics on viral infections.

Protecting Your Microbiome: Practical Steps You Can Take

While antibiotics can have disruptive effects, there are several steps you can take to mitigate the damage and support a healthy microbiome:<ul> <li>Probiotics: Consider taking a probiotic supplement during and after antibiotic treatment to help replenish beneficial bacteria. Look for a diverse blend of strains known to support gut health.</li> <li>Diet: Focus on a diet rich in fiber, fruits, vegetables, and fermented foods. These foods provide nourishment for beneficial bacteria and promote a balanced microbiome.</li> <li>Limit Processed Foods and Sugar: Minimize your intake of processed foods, sugary drinks, and artificial sweeteners, as these can negatively impact the gut microbiome.</li> <li>Talk to Your Doctor: Discuss the potential risks and benefits of antibiotics with your doctor and explore alternative treatment options when appropriate.</li> </ul>By taking proactive steps to protect your microbiome, you can minimize the potential long-term effects of antibiotics and support your overall health and 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 exactly is the microbiome, and why is it so important to my health?

The microbiome is a vast and complex ecosystem within our bodies, comprising trillions of microorganisms, including bacteria, viruses, fungi, and archaea. It's crucial for overall health, influencing digestion, immunity, and even mental well-being. Maintaining a balanced microbiome is essential because it prevents diseases and optimizes bodily functions. A healthy microbiome ensures efficient nutrient absorption, supports a strong immune system, and contributes to mental well-being. When the microbiome is imbalanced, it can lead to various health issues.

How do antibiotics disrupt the balance of the microbiome, and what are the potential consequences of this disruption?

Antibiotics, while effective against bacterial infections, can disrupt the microbiome by indiscriminately killing both harmful and beneficial bacteria. This disruption leads to an imbalance, potentially causing short-term issues like digestive problems and long-term consequences. Long-term effects may include increased susceptibility to infections, alterations in metabolism, and even impact on mental health. Antibiotics can also contribute to antibiotic resistance within the microbiome. The impact on the oral and gut viromes, specifically, can lead to changes in viral communities and the development of antibiotic resistance genes.

Can you explain the key differences between the oral virome and the fecal virome and how antibiotics affect them differently?

The study in PLOS One found significant differences between the oral and fecal viromes. The gut virome was more diverse and complex than the oral virome. Antibiotics' impact varied: in the oral cavity, an unexpected increase in papillomaviruses was observed, potentially linking antibiotic use to increased viral activity. In the gut, while overall diversity wasn't significantly impacted, there was an expansion of genes associated with antibiotic resistance. The study highlights how antibiotics can shape viral communities differently in the mouth and gut, with implications for oral and gut health. These effects underscore the need for strategies to protect and restore the microbiome after antibiotic use.

What practical steps can I take to protect and support my microbiome when I need to take antibiotics?

Several steps can help mitigate the impact of antibiotics and support a healthy microbiome. Consider taking probiotic supplements during and after antibiotic treatment to replenish beneficial bacteria. Focus on a diet rich in fiber, fruits, vegetables, and fermented foods. Fiber and these foods nourish the beneficial bacteria and promote a balanced microbiome. Minimize the intake of processed foods, sugary drinks, and artificial sweeteners, as these negatively affect the gut microbiome. Always discuss the risks and benefits of antibiotics with your doctor, exploring alternative treatment options when appropriate. These actions help minimize damage, promote the restoration of a balanced microbiome, and support overall health.

What are the implications of antibiotic-induced changes in the virome, specifically the increased presence of papillomaviruses and the expansion of antibiotic resistance genes?

The study's findings about virome changes, such as increased papillomaviruses in the oral cavity, raise concerns about the potential long-term effects of antibiotics on viral infections, potentially increasing the risk of certain health issues. The expansion of genes associated with antibiotic resistance in the gut virome is particularly concerning because it can reduce the effectiveness of antibiotics over time. This means that bacterial infections may become harder to treat. These changes emphasize the importance of cautious antibiotic use, along with proactive steps to protect and restore the microbiome, to safeguard both oral and gut health and maintain the effectiveness of antibiotic treatments.