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Agricultural companies might use Crispr to change existing genes in crops to create new traits. That might sidestep the regulations and controversy surrounding genetically engineered crops, which generally have foreign DNA added.

The development of the new tool is an example of the unanticipated benefits of basic research. About 15 years ago, after it became possible to sequence the entire genomes of bacteria, scientists noticed that many species had those repeated DNA sequences that were first noticed a decade earlier in Osaka. They were called “clustered regularly interspaced short palindromic repeats” — Crispr for short.

But what was their purpose? In 2007, researchers at Danisco, a company that supplies bacterial cultures used in making cheese and yogurt, confirmed hypotheses that Crispr protects bacteria from viruses.

It is part of an adaptive immune system — one that remembers a pathogen so it is ready the next time that same invader appears. The human adaptive immune system is why people get measles only once and why vaccines work. But it was not imagined that single-cell organisms like bacteria had such systems.

Here is how it works. The repeated DNA sequences in the bacterial genome are separated from one another by other sequences. These “spacers” are excerpts from the sequences of viruses that have attacked the bacterium or its ancestors. They are like genetic mug shots, telling the bacterium which bad guys to watch for. The Crispr defense system will slice up any DNA with that same sequence, so if the same virus invades again, it will be destroyed.

If a previously unseen virus attacks, a new spacer, a new mug shot, is made and put at the end of the chain.

That means the Crispr region “is like a tape recording of exposure to prior invaders,” said Erik J. Sontheimer, a Northwestern University professor who helped unravel the mechanism.

And it provides a way to tell two bacterial strains apart, because even two strains from the same species are likely to have encountered different viruses. This is already being used to identify sources of food-poisoning outbreaks.

Cheese and yogurt companies can examine Crispr regions to see if their bacterial cultures are immunized against particular viruses that could slow production.