east is not typically considered a domesticated organism. Dogs, cats, and cows might come to mind first, but humans have nonetheless played an important role in the fungus’s evolution. A study in Current Biology published yesterday (December 9) reports that humans have caused most bread yeast strains, Saccharomyces cerevisiae, to diverge into two distinct groups: one used in large-scale, industrial bread-making and one used in artisanal sourdough bread. While industrial strains start fermenting more quickly, sourdough yeasts have more copies of the genes responsible for metabolizing maltose, a process that typically happens later in the fermentation process and helps leaven the dough.
“It’s a good paper,” says Pacific Northwest Research Institute senior investigator Aimée Dudley, who studies yeast genetics and was not involved in the study. “It makes sense with what we know about how people have been baking bread historically,” referring to the priority of speed in commercial bread-making compared to that of artisanal bakers.
Bread is universal and has been for millennia, explains French National Research Institute for Agriculture evolutionary geneticist Delphine Sicard, a coauthor of the study, but with a dramatic shift toward mass-produced yeast starters in the industrial era, her team wanted to understand how these changes have shaped yeast’s evolution. Yeast domestication has been studied in other food and beverages—cheese, wine, and beer, for example—but not in breads. Sicard says bread yeasts have seldom been studied because many of these yeast strains are tetraploids, cells that contain four homologous sets of chromosomes, which makes studying their population genetics more complicated than studying diploids or haploids.
Historians and scientists have long theorized that beer brewers and bakers have historically exchanged their yeasts, and the results of the study add some weight to the idea.
Sicard’s team obtained 198 sourdough strains from France, Belgium, and Italy and 31 commercial strains from starter kits or international yeast collections. They analyzed the number of chromosome sets in each of these strains using flow cytometry and investigated the genetic diversity of diploids and tetraploids using microsatellite marker analysis. Sicard and her colleagues then analyzed the newly sequenced genomes of 17 bakery yeast strains and 1,011 other S. cerevisiae strains described in a 2018 Nature study, which includes 51 bakery strains, to create a phylogenetic tree and map copy number variations along it.
They found that sourdough strains typically contained a higher copy number of genes that encode proteins that transport and regulate maltase and isomaltase as well as the enzymes themselves, which break down the sugars maltose and isomaltose. Abnormalities in copy number can be harmful to cells, but the authors explain that they can also enable rapid adaptation in a period of stringent selection, such as proliferating in the toxic high–maltose and isomaltose environment of wheat flour that’s used in making sourdough bread.
The researchers found that, in a synthetic sourdough environment with only maltose as a carbon source, yeast that had more copies of these genes were more abundant by the end of fermentation than were yeasts that had fewer copies. Whether bakers deliberately passed on sourdough starters that they thought would work best or the yeast evolved to adapt to their environments, the end result is that sourdough yeast is well-suited for making specifically sourdough bread, explains Sicard. “This is a nice example of a domestication genetic signature,” Sicard says.
Meanwhile, industrial bakers appear to have selected yeasts that start fermentation more quickly—producing 1 g of carbon dioxide after inoculation about half an hour earlier than sourdough yeasts do, on average, in the study—prioritizing the breakdown of glucose over more complex sugars such as maltose and isomaltose that would take more time to break down. Both industrial and sourdough strains started fermentation more quickly than all other yeasts analyzed, including beer and wine strains.
Dudley points out that sourdough starter contains other microbes, such as lactic acid bacteria and other yeasts, that form complex interactions with the S. cerevisiae, so she says she hopes to see future work that examines these relationships to understand how they may be contributing to the domestication of S. cerevisiae.
With this renewed interest in sourdough bread, we may be able to conserve more microbial diversity in the future, at least in this food chain.—Delphine Sicard, French National Institute for Agriculture, Food, and Environment
Historians and scientists have long theorized that beer brewers and bakers have historically exchanged their yeasts, and the results of the study add some weight to the idea: a group of yeast strains that the researchers in the Nature study associated with African beer contains sourdough strains isolated from Ghanaian maize dough, suggesting that the same strains were historically used both to ferment maize dough and to brew beer. Sicard and her colleagues also report that another clade identified in the Nature study contains beer strains, commercial bakery strains from all over the world, and a few of the newly sequenced sourdough strains from Belgium and France. Meanwhile, all but three bakery strains clustered separately from wine and sake lineages, suggesting distinct evolutionary histories.
Yeast is found just about everywhere, making it a daunting task to categorize yeast strains, says Edward Louis, the director of the Centre for Genetic Architecture of Complex Traits at the University of Leicester who was not involved in the latest study. Only approximately two-thirds of the analyzed yeast strains Sicard’s team analyzed could be grouped into the industrial and artisanal sourdough clades—and even among these, there were many “mosaic strains” that included characteristics of both.
“Is there really domestication or are we just taking advantage of natural variation that’s out there or moving yeast around to generate new diversity that just happens to fit whatever environment we’re throwing at them?” Louis asks. Still, he says the finding about the quick rate of fermentation among the industrial strains is compelling evidence, as those properties most likely wouldn’t give yeast an advantage on oak tree bark or soil, where S. cerevisiae is found in the wild, for example.
Sicard says she worries that industrial bread-making could lower the amount of diversity found in yeast strains, but that she is encouraged by the resurgence of homemade bread baking over the past decade, and especially during the COVID-19 pandemic. “With this renewed interest in sourdough bread, we may be able to conserve more microbial diversity in the future, at least in this food chain,” she says. “It’s tough to make bread, and if we can, as scientists, add value to bakers’ work, then it would be great.”
Louis says that this study helps capture the genetic diversity of bread yeasts, which is an important step toward preserving it. “By going the commercial route and replacing it all with one or two types, we’ll still have good bread and beer, but we’re probably losing a lot of the nice things about it,” he says.
F. Bigey et al., “Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes,” Current Biology, doi:10.1016/j.cub.2020.11.016, 2020.