On Mar. 18, 2025, an interdisciplinary group of researchers from Rice University announced they have created a new synthetic biology RNA “barcoding” tool to track genetic exchanges in microbial communities, providing new insights into how genes move across species.

In the microscopic world of bacteria, gene transfer is a powerful mechanism that can alter cellular function, drive and even shape entire ecosystems.

Traditional methods for studying gene transfer involve labeling mobile genetic elements with fluorescent proteins or antibiotic resistance genes. While effective, these approaches require isolating and growing microbes in a lab, limiting their use in complex environments.

The Rice team’s new method, called RNA-addressable modification (RAM), bypasses these hurdles by using a synthetic catalytic RNA (cat-RNA) to “barcode” ribosomal RNA (rRNA) inside living cells.

By writing genetic information directly into the 16S rRNA — a molecule universally found in bacteria — the researchers could track which microbes acquired foreign DNA without disrupting their natural environment. Additionally, as targeted sequencing of 16S rRNA is the gold standard for identifying different species of bacteria, this method can leverage established and easy to use protocols and analysis software.

The study also showed that RAM can be used to measure differences in host ranges between DNA plasmid types. With tens of thousands of different DNA plasmids found in natural environmental microbes, RAM provides an easy and cost-effective method to begin to understand the relationship between plasmids and their hosts.

The findings were recently published in Nature Biotechnology.