Humans have domesticated plants and animals since the early days of civilization, changing the life cycles, appearances and behaviors of crops and livestock. A new study shows humans have done the same to fermented products, selectively taming microbes. But as a result, microbial strains have evolved to where they can no longer survive in the wild.
“The burst of flavor from summer’s first sweet corn and the proud stance of a show dog both testify to the power of domestication,” reads an article in Science titled “Humans tamed the microbes behind cheese, soy, and more.” “But so does the microbial alchemy that turns milk into cheese, grain into bread, and soy into miso. Like the ancestors of the corn and the dog, the fungi and bacteria that drive these transformations were modified for human use. And their genomes have acquired many of the classic signatures of domestication.”
Humans have used selective breeding to produce the most desired traits in plants and animals – for example, making a plant less bitter or an animal larger. Thousands of years of domestication have changed DNA. Though microbes can’t be bred the same way, “humans can grow microbes and select variants that best serve our purposes.” It’s now left “genetic hallmarks similar to those in domesticated plants and animals: The microbes have lost genes, evolved into new species or strains and become unable to thrive in the wild.”
Scientists shared this research during two talks at Microbe 2022, the annual meeting of the American Society for Microbiology in Washington D.C. The talks – “Origins and Consequences of Microbial Strain Diversity” and “Microbial Diversity in Food Systems: From Farm to Fork”
– were convened by TFA Advisory Board members Benjamin Wolfe, PhD, ofTufts University, and Josephine Wee, PhD, from Penn State. They invited various academics to present their research on these topics.
Microbial Domestication in Cheese
Wolfe said the studies “are getting to the mechanisms” of how microbial domestication works. They reveal “which genes are key to microbes’ prized traits – and which can be lost,” continues the Science article. This work is critical to the future of food, as these microbe gene traits can shape fermented foods and beverages.
Presenters included Vincent Somerville, PhD, from the University of Lausanne, Switzerland, speaking on the changing genomic structure of cheese cultures. He pointed out that bread yeasts have long been domesticated. They’ve lost so much of their genetic variation that they can’t live in the wild. Other microbes are “lacking clear evidence of domestication … in part because [their] microbial communities can be hard to study,” he said.
Somerville’s research revolves around a starter culture for a Swiss hard cheese. Bacterial cheese starters were created by early cheesemakers; in the 70s, samples of these cultures began being banked to ensure quality. But Somerville and his collaborators, after sequencing the genomes of more than 100 of these samples, found little genetic diversity, with just a few strains of two dominant species..
“The exciting thing from this work was having samples over time,” Wolfe said. “You can see the shaping of diversity,” with changes in the past 50 years hinting at the trajectory of change over past centuries.
Domesticated vs. Wild Aspergillus
John Gibbons, a genomicist at the University of Massachusetts, Amherst, presented on Aspergillus oryzae, “the fungus that jump-starts production of sake from rice, and soy sauce and miso from soybeans.” Farmers cultivate A. oryzae, which reproduces on its own. “But when humans take a little finished sake and transfer it to a rice mash to begin fermentation anew, they also transfer cells of the fungal strains that evolved and survived best during the first round of fermentation,” the article reads.
Gibbons compared the genomes of A. oryzae strains with those of A. flavus, it’s wild ancestor. Human involvement in transferring the fungus has “boosted A. oryzae’s ability to break down starches and to tolerate the alcohol produced by fermentation.” The domesticated Aspergillus strains may have up to five times the number of genes used to break down starches compared to their ancestors.
“The restructuring of metabolism appears to be a hallmark of domestication in fungi,” he said.
Gibbons also found the genes of domesticated A. oryzae to have little variation. And some key genes have disappeared, “including those for toxins that would kill the yeast needed to complete fermentation — and which can make humans sick.” The article concludes: “Domestication has apparently made A. oryzae more human friendly, just as it bred bitter flavors out of many food plants.”