Scientists have long known that bacteriophages, viruses that infect bacteria, live in our gut, but exactly what they do has remained elusive.
Researchers developed a clever mouse model that can temporarily eliminate these phages without harming the bacteria, using a UTI treatment ingredient called acriflavine. Their experiments showed that without phages, gut bacteria become less sensitive to antibiotics, suggesting that these tiny viruses might actually worsen the microbiome damage antibiotics cause. This surprising connection could lead to new breakthroughs in gut health research.
Gut Viruses: The Overlooked Partners of Bacteria
Some things are just meant to be together: peanut butter and jelly, salt and pepper — and in your gut, bacteria and the viruses that infect them.
These viruses, known as bacteriophages, naturally target the bacterial species living in your digestive system. Although phages have evolved alongside bacteria for millions of years, they remain far less understood. They’re tricky to classify and so closely intertwined with their bacterial hosts that scientists still aren’t sure exactly what roles they play.
But what if researchers could compare a gut microbiome with and without these viruses, under otherwise identical conditions?
A New Way to Study Phages
At Virginia Tech, biologist Bryan Hsu and his team figured out how to do just that.
Hsu and graduate student Hollyn Franklin developed a model that can selectively remove bacteriophages from a mouse’s gut microbiome — and later restore them — without disturbing the bacteria themselves. In early tests of the model, the researchers found intriguing evidence that phages might actually make gut bacteria more sensitive to antibiotics. Their findings were published today (April 28) in the journal Cell Host & Microbe.
Acriflavine: The Phage-Silencing Compound
What could inhibit a bacteria’s viruses but not the bacteria itself? In her early search through the literature, Franklin found a chemical compound called acriflavine that fit the bill. It’s a component of a widely available medication used in Brazil to treat urinary tract infections (UTI).
Fortuitously, a member of Hsu’s lab and paper co-author, Rogerio Bataglioli, is a native Brazilian. He shipped a massive order of acriflavine to his parent’s house. But he forgot to tell his parents it was coming, Hsu said.
“His mom called, and asked, ‘Is everything OK? Because 20 boxes of UTI treatment just arrived under your name.’”
From UTI Medicine to Breakthrough Experiment
After that was sorted, Franklin began administering acriflavine to lab mice. Over a period of 12 days, there was a dramatic reduction in the concentration of viral particles. And they didn’t bounce back when she stopped administering the drug.
But when Franklin reintroduced a tiny sample of the mouse’s own gut microbiome, extracted before treatment, the natural phage populations sprang back to life.
“It went away when we wanted it to, and came back when we wanted it to,” said Hsu. “Which means we have a bacteriophage conditional mouse model.”
Or, more fun: BaCon mouse model.
The Power of a Switchable Microbiome
To see if the mouse model had some significance for health, Hsu’s research team went straight to one of the hottest topics in the field: the collateral damage that antibiotics have on a patient’s resident microbial population.
Antibiotics save millions of lives every year, but the drug rages indiscriminately through bad, benign, and beneficial bacteria alike, disrupting our gut microbiome and leaving us vulnerable to new pathogens.
Antibiotics, Gut Microbes, and Phage Interference
Could phages be playing a role in the destructive wake of an antibiotic treatment? Hsu and Franklin used their BaCon mouse model to ask this question and administered antibiotics to mice with and without phage populations.
Their results suggest that phages increase the sensitivity of bacteria to antibiotics.
“It’s hard to make definitive conclusions, but these results are telling us that phages have some significance for how we respond to antibiotics,” Hsu said.
Phages: Potential Game Changers in Microbiome Health
The next questions, according to Franklin, will explore if phages caused these effects or are simply correlated with them, and what role phages play in diseases, which would open new doors in microbiome studies.
Answers may be served with a side of BaCon mouse.
Reference: 28 April 2025, Cell Host & Microbe.
Funding for this work was provided by the Virginia Tech Institute for Critical Technology and Applied Science, the National Institute of General Medical Sciences of the National Institutes of Health.
Research collaborators include:
- Frank Aylward, associate professor of biological sciences
- Anh Ha, postdoctoral research associate
- Rita Makhlouf, graduate student, biological sciences
- Zachary Baker, graduate student, biological sciences
- Sydney Murphy ´24, former undergraduate researcher in the Hsu Lab
- Hannah Jirsa ´23, former undergraduate researcher in the Hsu Lab
- Joshua Heuler, graduate student, biological sciences
- Teresa Southard, associate professor of anatomic pathology
News
Scientists Flip a Gut Virus “Kill Switch” – Expose a Hidden Threat in Antibiotic Treatment
Scientists have long known that bacteriophages, viruses that infect bacteria, live in our gut, but exactly what they do has remained elusive. Researchers developed a clever mouse model that can temporarily eliminate these phages [...]
Enhanced Antibacterial Polylactic Acid-Curcumin Nanofibers for Wound Dressing
Background Wound healing is a complex physiological process that can be compromised by infection and impaired tissue regeneration. Conventional dressings, typically made from natural fibers such as cotton or linen, offer limited functionality. Nanofiber [...]
Global Nanomaterial Regulation: A Country-by-Country Comparison
Nanomaterials are materials with at least one dimension smaller than 100 nanometres (about 100,000 times thinner than a human hair). Because of their tiny size, they have unique properties that can be useful in [...]
Pandemic Potential: Scientists Discover 3 Hotspots of Deadly Emerging Disease in the US
Virginia Tech researchers discovered six new rodent carriers of hantavirus and identified U.S. hotspots, highlighting the virus’s adaptability and the impact of climate and ecology on its spread. Hantavirus recently drew public attention following reports [...]
Studies detail high rates of long COVID among healthcare, dental workers
Researchers have estimated approximately 8% of Americas have ever experienced long COVID, or lasting symptoms, following an acute COVID-19 infection. Now two recent international studies suggest that the percentage is much higher among healthcare workers [...]
Melting Arctic Ice May Unleash Ancient Deadly Diseases, Scientists Warn
Melting Arctic ice increases human and animal interactions, raising the risk of infectious disease spread. Researchers urge early intervention and surveillance. Climate change is opening new pathways for the spread of infectious diseases such [...]
Scientists May Have Found a Secret Weapon To Stop Pancreatic Cancer Before It Starts
Researchers at Cold Spring Harbor Laboratory have found that blocking the FGFR2 and EGFR genes can stop early-stage pancreatic cancer from progressing, offering a promising path toward prevention. Pancreatic cancer is expected to become [...]
Breakthrough Drug Restores Vision: Researchers Successfully Reverse Retinal Damage
Blocking the PROX1 protein allowed KAIST researchers to regenerate damaged retinas and restore vision in mice. Vision is one of the most important human senses, yet more than 300 million people around the world are at [...]
Differentiating cancerous and healthy cells through motion analysis
Researchers from Tokyo Metropolitan University have found that the motion of unlabeled cells can be used to tell whether they are cancerous or healthy. They observed malignant fibrosarcoma [...]
This Tiny Cellular Gate Could Be the Key to Curing Cancer – And Regrowing Hair
After more than five decades of mystery, scientists have finally unveiled the detailed structure and function of a long-theorized molecular machine in our mitochondria — the mitochondrial pyruvate carrier. This microscopic gatekeeper controls how [...]
Unlocking Vision’s Secrets: Researchers Reveal 3D Structure of Key Eye Protein
Researchers have uncovered the 3D structure of RBP3, a key protein in vision, revealing how it transports retinoids and fatty acids and how its dysfunction may lead to retinal diseases. Proteins play a critical [...]
5 Key Facts About Nanoplastics and How They Affect the Human Body
Nanoplastics are typically defined as plastic particles smaller than 1000 nanometers. These particles are increasingly being detected in human tissues: they can bypass biological barriers, accumulate in organs, and may influence health in ways [...]
Measles Is Back: Doctors Warn of Dangerous Surge Across the U.S.
Parents are encouraged to contact their pediatrician if their child has been exposed to measles or is showing symptoms. Pediatric infectious disease experts are emphasizing the critical importance of measles vaccination, as the highly [...]
AI at the Speed of Light: How Silicon Photonics Are Reinventing Hardware
A cutting-edge AI acceleration platform powered by light rather than electricity could revolutionize how AI is trained and deployed. Using photonic integrated circuits made from advanced III-V semiconductors, researchers have developed a system that vastly [...]
A Grain of Brain, 523 Million Synapses, Most Complicated Neuroscience Experiment Ever Attempted
A team of over 150 scientists has achieved what once seemed impossible: a complete wiring and activity map of a tiny section of a mammalian brain. This feat, part of the MICrONS Project, rivals [...]
The Secret “Radar” Bacteria Use To Outsmart Their Enemies
A chemical radar allows bacteria to sense and eliminate predators. Investigating how microorganisms communicate deepens our understanding of the complex ecological interactions that shape our environment is an area of key focus for the [...]
