EMERYVILLE, Calif. — Vanilla, saffron, patchouli. For centuries, spices and flavorings like these have come from exotic plants growing in remote places like the jungles of Mexico or the terraced hillsides of Madagascar. Some were highly prized along ancient trading routes like the Silk Road.

Now a powerful form of genetic engineering could revolutionize the production of some of the most sought-after flavors and fragrances. Rather than being extracted from plants, they are being made by genetically modified yeast or other micro-organisms cultured in huge industrial vats.

“It’s just like brewing beer, but rather than spit out alcohol, the yeast spits out these products,” said Jay D. Keasling, a co-founder of Amyris, a company based here that is a pioneer in the field. However, while yeast makes alcohol naturally, it would not produce the spices without the extensive genetic rejiggering, which is called synthetic biology.

The advent of synthetic biology raises thorny economic and regulatory issues, such as whether such yeast-made ingredients can be called natural and whether developing countries dependent on these crops will be hurt.