Photos from Eadweard Muybridge’s study of a galloping horse have been recorded in bacterial DNA Eadweard Muybridge/The LIFE Picture Collection/Gett

Life is an open book and we’re writing in it. A team at Harvard University has used the CRISPR genome-editing tool to encode video into live bacteria – demonstrating for the first time that we can turn microbes into librarians that can pass records on to their descendants – and perhaps to ours.

The technique could even let us create populations of cells that keep their own event logs, making records as biological processes like disease or brain development happen.

DNA is one of the best media for storing data we know of. Researchers have already crammed large amounts of information from books to digital images into tiny amounts of biological material. In theory, a gram of single-stranded DNA can encode 455 exabytes, or roughly 100 billion DVDs.


Ordered existence

Most previous DNA storage work has used artificial DNA: digital information is translated into a DNA sequence that is then synthesized.

However, using CRISPR lets you cut and paste the digital information directly into the DNA of a live organism, in this case a large population of E. coli.

Bacteria use the CRISPR/Cas9 system to record information in their DNA about viruses they encounter. And this machinery has been co-opted by researchers to enable us to precisely edit genomes.

In bacteria, each new entry gets stored upstream of the last one, which makes it possible to read off a history of events in the order they happened. Previous groups have created lifelogging cells by using CRISPR/Cas9 to mark the genome when a particular event occurs. But these marks just provide a tally of how many times something happens.

Getting animated

Seth Shipman at Harvard University and his colleagues have now used a version of CRISPR with a different enzyme, called CRISPR/Cas1-Cas2. This let them add a message to the genome rather than simply cut a notch.

The message was a recorded image of a human hand and five images showing a galloping horse, taken from Eadweard Muybridge’s 1878 photographic study of the animal’s motion, which has since been animated.

An image of a hand (left) was stored in living bacteria, and then after multiple generations, the image on the right was recovered by sequencing bacterial genomes Seth Shipman

To get the DNA sequences encoding this data inside the cells, the team applied an electrical current that opened channels in the cells’ walls and the DNA flowed in. Once inside, CRISPR got to work.

To read the data back again, the team sequenced the DNA of more than 600,000 cells. The large number is necessary because most cells will not have edited their genome entirely accurately. “Every cell isn’t going to acquire every piece of information we throw at it,” says Shipman. The more cells that are sampled, the better the reconstruction of the data. Fortunately, with modern sequencing tools, reconstruction is quick.

The five frames of a horse in motion showed that it is possible to capture data chronologically and replay them as a video. “You get a physical record of events over time,” says Shipman. For a long time we wanted to have some way of storing timing information inside cells, says Shipman. “The CRISPR system is perfectly adapted to that.”

Book of life

“This is a really neat paper,” says Yaniv Erlich at Columbia University in New York. The team didn’t store that much data and it is not clear that the CRISPR technique can compete with the storage capacity of synthetic DNA. But inserting information into living cells opens up a lot of possibilities, he says.

For a start, it lets you add to or change the stored information later. And because the data is written into the bacterial genomes, it gets passed down between generations. Mutations happen, but not nearly as many as you think, says Shipman – certainly not enough to corrupt the data stored across a large population of cells.

Storing data in bacteria could even be a way to make important information survive a nuclear apocalypse. You could use Deinococcus radiodurans, a species that maintains its genome in extreme radiation conditions, says Erlich.

Shipman wants to turn cells into recording devices that document what takes place inside themselves. He is excited about the possibility of keeping a log book of events inside a living brain as it develops, showing how different brain cells acquire their distinct identities.

“It’s hard to understand what events make brain cells fully defined,” says Shipman. “You can’t easily get in there to take a look. Taking a brain apart disrupts the whole process.”

You could also get a cell to diarise what happens as it changes from healthy to diseased. Now that would be an account worth reading.

Journal reference: Nature, DOI: 10.1038/nature23017