Gene transfer is an important mechanism used by bacteria to exchange genetic material. This can allow these microorganisms to adapt to different ecosystems and develop antibiotic resistance. A team of interdisciplinary researchers from Rice University created a new method using RNA barcoding to monitor gene transfers within microbial communities.
“We’ve long known that bacteria swap genes in ways that impact human health, biotechnology, and environmental stability,” stated James Chappell, associate professor of biosciences and bioengineering. “But mapping which microbes participate in gene transfer has been challenging. This new technique gives us a direct way to record this information inside the cells themselves.”
Conventional approaches to studying gene transfer typically involve tagging mobile genetic elements with fluorescent proteins or antibiotic-resistance markers. Despite their effectiveness, these techniques require microbial isolation and cultivation in a laboratory, reducing their feasibility in complex settings. In response to this challenge, the research team utilized their diverse expertise to invent a new synthetic biology tool.
RNA-addressable modification (RAM), the new technique developed by the Rice team, avoids these barriers by utilizing a synthetic catalytic RNA (cat-RNA) to “barcode” ribosomal RNA (rRNA) within living cells. Through direct genetic encoding in the 16S rRNA, a molecule found in all bacteria, the team was able to observe microbial acquisition of foreign DNA while leaving their environment undisturbed. Furthermore, because targeted sequencing of 16S rRNA is the benchmark for bacterial species identification, this method can capitalize on well-established and user-friendly protocols and analysis software.
“This is a game-changer for creating a mobile DNA atlas,” noted Joff Silberg, the Stewart Memorial Professor of biosciences and professor of bioengineering. “Instead of writing information randomly in bacterial DNA, which is permanent and arduous to read out, we write information in a region of RNA that is highly conserved across the tree of life, making the information cheap and easy to read out.”
To achieve this, the team designed a small catalytic RNA (ribozyme-based RNA) capable of attaching a unique barcode to 16S rRNA during gene transfer. This cat-RNA was transferred into a model microbial community using conjugative plasmids, which serve as natural vectors for gene exchange in bacteria. In the experiment, barcoding plasmids were introduced into E. coli donor bacteria, which subsequently transferred their genetic material to diverse microbes within a wastewater community. Following a 24-hour incubation, the researchers collected total RNA and performed sequencing on the barcoded 16S rRNA.
“What we saw was remarkable,” emphasized Lauren Stadler, associate professor of civil and environmental engineering. “Around half of the bacterial taxa in the wastewater community could pick up the plasmids, giving us a detailed map of horizontal gene transfer events.”
Findings from the study also showed that RAM can help assess variations in host ranges between different types of DNA plasmids. Given the vast diversity of DNA plasmids in environmental microbes, RAM provides an accessible and economical method for studying plasmid-host interactions.
The RAM method has broad applications in medicine, biotechnology, and environmental science. It can track antibiotic resistance, aid bioremediation by engineering microbiomes, and enable controlled gene transfer in synthetic biology. Future advancements may expand its use to other gene exchange mechanisms and improve resolution by enhancing cat-RNA stability and barcode diversity.
“With further development, RNA barcoding could become a universal tool for storing information in environmental communities about additional microbial behaviors beyond gene transfer,” Silberg stated.
Publication Details
Kalvapalle, P.B., Staubus, A., Dysart, M.J. et al. Information storage across a microbial community using universal RNA barcoding. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02593-0
“We’ve long known that bacteria swap genes in ways that impact human health, biotechnology, and environmental stability,” stated James Chappell, associate professor of biosciences and bioengineering. “But mapping which microbes participate in gene transfer has been challenging. This new technique gives us a direct way to record this information inside the cells themselves.”
Conventional approaches to studying gene transfer typically involve tagging mobile genetic elements with fluorescent proteins or antibiotic-resistance markers. Despite their effectiveness, these techniques require microbial isolation and cultivation in a laboratory, reducing their feasibility in complex settings. In response to this challenge, the research team utilized their diverse expertise to invent a new synthetic biology tool.
RNA-addressable modification (RAM), the new technique developed by the Rice team, avoids these barriers by utilizing a synthetic catalytic RNA (cat-RNA) to “barcode” ribosomal RNA (rRNA) within living cells. Through direct genetic encoding in the 16S rRNA, a molecule found in all bacteria, the team was able to observe microbial acquisition of foreign DNA while leaving their environment undisturbed. Furthermore, because targeted sequencing of 16S rRNA is the benchmark for bacterial species identification, this method can capitalize on well-established and user-friendly protocols and analysis software.
“This is a game-changer for creating a mobile DNA atlas,” noted Joff Silberg, the Stewart Memorial Professor of biosciences and professor of bioengineering. “Instead of writing information randomly in bacterial DNA, which is permanent and arduous to read out, we write information in a region of RNA that is highly conserved across the tree of life, making the information cheap and easy to read out.”
To achieve this, the team designed a small catalytic RNA (ribozyme-based RNA) capable of attaching a unique barcode to 16S rRNA during gene transfer. This cat-RNA was transferred into a model microbial community using conjugative plasmids, which serve as natural vectors for gene exchange in bacteria. In the experiment, barcoding plasmids were introduced into E. coli donor bacteria, which subsequently transferred their genetic material to diverse microbes within a wastewater community. Following a 24-hour incubation, the researchers collected total RNA and performed sequencing on the barcoded 16S rRNA.
“What we saw was remarkable,” emphasized Lauren Stadler, associate professor of civil and environmental engineering. “Around half of the bacterial taxa in the wastewater community could pick up the plasmids, giving us a detailed map of horizontal gene transfer events.”
Findings from the study also showed that RAM can help assess variations in host ranges between different types of DNA plasmids. Given the vast diversity of DNA plasmids in environmental microbes, RAM provides an accessible and economical method for studying plasmid-host interactions.
The RAM method has broad applications in medicine, biotechnology, and environmental science. It can track antibiotic resistance, aid bioremediation by engineering microbiomes, and enable controlled gene transfer in synthetic biology. Future advancements may expand its use to other gene exchange mechanisms and improve resolution by enhancing cat-RNA stability and barcode diversity.
“With further development, RNA barcoding could become a universal tool for storing information in environmental communities about additional microbial behaviors beyond gene transfer,” Silberg stated.
Publication Details
Kalvapalle, P.B., Staubus, A., Dysart, M.J. et al. Information storage across a microbial community using universal RNA barcoding. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02593-0