Researchers have converted a natural bacterial immune system into a microscopic data recorder, laying the groundwork for a new class of technologies that use bacterial cells for everything from disease diagnosis to environmental monitoring.

Using CRISPR-Cas, an immune system in many species of bacteria, researchers engineered human gut microbe Escherichia coli or E. coli to act as data recorders while they move through the body. "The CRISPR-Cas system is a natural biological memory device," said Harris Wang, Assistant Professor at the Columbia University Medical Center. "From an engineering perspective that's actually quite nice, because it's already a system that has been honed through evolution to be really great at storing information," Wang added.

Whenever a bacteria survives an encounter with a attacking viruses, CRISPR-Cas copies a snippet of the invader's DNA. As a result, if the same viruses try to infect again, the CRISPR-Cas system can recognise, even generations later, and eliminate them. "Such bacteria, swallowed by a patient, might be able to record the changes they experience through the whole digestive tract, yielding an unprecedented view of previously inaccessible phenomena," Wang said, in the paper described in the journal Science.

Other applications could include environmental sensing and basic studies in ecology and microbiology, where bacteria could monitor otherwise invisible changes without disrupting their surroundings. To build their microscopic recorder, the researchers modified a piece of DNA called a plasmid, giving it the ability to create more copies of itself in the bacterial cell in response to an external signal. A separate recording plasmid, which drives the recorder and marks time, expresses components of the CRISPR-Cas system. 

The researchers could then examine the bacterial CRISPR locus and use computational tools to read the recording and its timing. The study proves the system can handle at least three simultaneous signals and record for days. CRISPR has been previously used to store poems, books, and images in DNA, but this is the first time its been used to record cellular activity and the timing.