While there’s still much left to be understood about the 100 trillion microorganisms living in our guts, recent discoveries point to potential new and unorthodox ways to fight viruses.

You may not think about what’s going on inside your intestines very often, especially if you’re healthy and feeling well.

But, if you are, you can thank your guts for that.

There are 10 times more microorganisms in your intestines than there are cells in your body. And scientists are at the tip of the iceberg in understanding how all of these interact to help digest food, synthesize vitamins, and ward off disease.

One finding in 2014 was how disrupting our sleep patterns with jet lag or shift work can disrupt the microorganisms in our intestines. This disruption can lead to obesity and glucose intolerance associated with diabetes.

Read More: Gut Bacteria Tells You When You’re Full »

A new paper, published in the journal Science, examines existing knowledge about the interactions of the transkingdom, or the trillions of bacteria, viruses, fungi, immune cells, and other organisms that make up your gut.

While scientists are exploring the gaps in knowledge of what they understand about the transkingdom, they know most about the multitudes of bacteria than other intestinal organisms.

Researchers Julie Pfeiffer of the University of Texas Southwestern Medical Center in Dallas and Herbert Virgin of the Washington University School of Medicine in St. Louis, note there are numerous ways bacteria can influence viral infections.

“A key direction for the field is to identify functional relationships governing transkingdom interactions in the intestine, including the dynamic coevolved relationship between the intestinal microbiota and innate and adaptive immunity,” they wrote.

Viruses, the researchers say, can use proteins from neighboring bacteria to protect themselves against the hostile, acidic environment of the intestines. It’s one of many ways these bugs are able to stay in our bodies and not be flushed out during a bowel movement.

Bacteria can also influence a virus’ immunity by using their antibodies, the proteins that help identify and remove unwanted invaders.

Read More: Could Balancing Our Gut Bacteria Be The Key to Unlocking RA? »

In digging through knowledge of the gut, Pfeiffer and Virgin say the most striking evidence is the recent discovery how bacteria affects the signaling of immune cells.

This suggests that antibiotics could help prevent a viral infection, which essentially goes in the face of how modern medicine fights unwanted viruses and bacteria.

Anyone who’s taken a biology course knows antibiotics don’t kill viruses, even though some doctors will still prescribe antibiotics for viral infections like the common cold.

Pfeiffer and Virgin, however, still advise against using antibiotics for this purpose until scientists have a better understanding of the interactions between viruses and bacteria.

The overuse and misuse of antibiotics, among other factors, have given rise to bacteria that have developed defenses against modern medicine. One of them, c. difficile, can take over the flora in your gut following antibiotics and cause potentially lethal diarrhea.

While great advances have been made in the understanding of the interactions going on our guts, Pfeiffer and Virgin stress more studies need to be done not just on how one virus affects one bacteria but rather how members of the transkingdom interact with one another.

“This simple concept has broad implications for prevention and therapy of viral infections of great medical importance,” researchers concluded in their paper.

Previous research out of Rockefeller University has investigated using viruses against antibiotic-resistant bacteria. They’ve identified a weak point in bacterial armor that would allow a virus to enter and kill the bacteria without giving it a chance to develop resistance to it.

Read More: Using Nature Against Itself to Make New Antibiotics »