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Sake, soy sauce, and the taming of the microbes

Cell Press

We all know that humans have domesticated plants and animals for our sustenance and enjoyment, but we've tamed various microbes as well. Now researchers reporting online on July 12 in Current Biology, a Cell Press publication, show that the mark of that domestication on microbes, and specifically on the mold used for thousands of years to brew sake and soy sauce from rice and soybeans, looks rather unique.

While changes brought by domestication to plants and animals have rested largely on exaggerating physical traits, changes to microbes have occurred instead via extensive remodeling of metabolism, the new evidence shows.

"We were quite surprised to see that secondary metabolism, the part responsible for producing toxins and other small organic molecules that fungi use for defense, was quite suppressed in the domesticated fungus, but not in its wild relative," said Antonis Rokas of Vanderbilt University. "Because the making of sake requires that both Aspergillus oryzae, the fungus that breaks down the rice starch into sugar, and Saccharomyces cerevisiae, the yeast that turns the sugar into alcohol, coexist, we think that the domestication process has produced a microbe that is 'friendly' to its other microbial coinhabitants."

Rokas' team systematically examined functional variation in the genomes of the domesticated Aspergillus oryzae and its wild and pathogenic relative A. flavus. That comparison revealed dramatic changes at the level of genes and their protein products, particularly those involved in metabolic pathways. The data show that domestication of the fungi led to their gradual evolution into "cell factories" for enzymes and metabolites needed for breaking complex carbohydrates into simple sugars.

It is highly likely that domestication of Aspergillus occurred via a mix of intention and accident, Rokas says. Simply by harvesting and reusing molds that gave rise to a successful batch, ancient brewers would have selected those best suited to the job.

"Remarkably, although the historical record for the use of microbes in the making of a 'wine'-like beverage dates back 7 to 9 millennia, it was not until Leeuwenhoek's discovery of microorganisms in 1675 that people fully realized what these were," Rokas says.

Rokas hopes that the new findings will lead to a greater appreciation of our microbial collaborators. Clearly, they deserve it. "Can one imagine the modern world without bread, yogurt, cheese, or alcoholic beverages?" he asks. Maybe one could, but why would they want to?


Gibbons et al.: "The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae."

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