Humans tamed the germs behind cheese, soy and more | science

The burst of flavor from the first sweet corn of summer and the proud stance of a show dog testify to the power of domestication. But so does the microbial alchemy that turns milk into cheese, grain into bread, and soy into miso. Like the ancestors of 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 signs of domestication, researchers reported in two talks this month at a meeting in Washington, DC.

Microbes cannot be “bred” in the normal sense because, unlike peas or pigs, individual microbes with desired traits cannot be selected and mated. But humans can grow microbes and select variants that better serve our purposes. Studies show that the process, repeated over thousands of years, has left genetic marks similar to those of domesticated plants and animals: microbes have lost genes, evolved into new species or strains, and become unable to thrive in the wild. .

Studies are “getting to the mechanisms” of how microbial mitigation works, says Benjamin Wolfe, a microbiologist at Tufts University. By finding out which genes are key to valuable microbial traits – and which may be lost – the work could help further improve the organisms that make up much of our food and drink, “especially [with] increased interest in fermented foods,” says microbial ecologist Ariane Peralta of East Carolina University.

Yeasts used to make bread have long been seen as domesticated because they have lost genetic variation and cannot live in the wild. But for other microbes, scientists “lack clear evidence of domestication … in part because [their] microbial communities can be difficult to study,” says graduate student Vincent Somerville of the University of Lausanne.

Somerville and John Gibbons, a genomicist at the University of Massachusetts, Amherst, independently focused on food fermentation, which helped early farmers and ranchers transform fresh produce and milk into products that could last for months or years. . Gibbons took a closer look at the genome Aspergillus oryzaedancing mushrooms—start making sake from rice and soy sauce and miso from soybeans.

When farmers cultivate A. oryzae, the fungus – a eukaryote, with its DNA enclosed in a nucleus – reproduces itself. But when people take some finished sake and transfer it to a rice mash to start fermentation again, they also transfer the cells of the fungal strains that evolved and survived best during the first round of fermentation.

Gibbons compared the genomes of the results of A. oryzae strains with those of their wild ancestors, A. flavus. Over time, he found, selection by humans had increased A. oryzaeits ability to break down starch and tolerate the alcohol produced by fermentation. “Metabolism restructuring appears to be a hallmark of fungal domestication,” he reported last week at Microbe 2022, the annual meeting of the American Society for Microbiology. For example, domesticated Aspergillus strains can have up to five times as many copies of a starch-metabolizing gene as their ancestors—”a great way for evolution to turn this enzyme on,” says Wolfe.

Tamed genes A. oryzae it also shows little variation, and the genome has lost several key genes, including those for toxins that would kill the yeast needed to complete fermentation—and that could make people sick. The softening apparently did A. oryzae friendlier to humans, as it extracted bitter tastes from many edible plants.

Somerville reported at the meeting that he has seen much the same pattern in prokaryotes, or organisms without a nucleus, including the bacteria used to make cheese. Early cheesemakers created bacterial “starter” cultures, which people in Switzerland use to make Gruyère and other cheeses. Since the 1970s, cheesemakers have collected samples of their starter cultures to evaluate their cheese and maintain high quality. Somerville sequenced the genomes of more than 100 samples.

“The exciting thing about this work was having samples over time,” says Wolfe. “You can see the diversity shaping,” with changes in the past 50 years hinting at the trajectory of change over the past centuries.

All samples had low genetic diversity, with only a few strains of two dominant species, Somerville reported. These few persistent types are probably important to the quality of the cheese, Gibbons said. The crops had also lost genes since the 1970s, including some needed to produce certain amino acids, which are required to assemble proteins. But amino acids are expensive to make – and these microbes live in protein-rich milk. “They were able to get rid of a bunch of genes they didn’t need,” says Wolfe. Somerville also found extensive gene exchange between microbes, a way to acquire new genes.

Putting the studies together, Gibbons concludes that the genomes of “domesticated prokaryotes and microbial eukaryotes are very similar” to each other and to domesticated multicellular organisms. Peralta cautions that the analogy with crops and animals is not perfect. Microbes can evolve much faster and thus can more easily “evolve”. Still, as researchers fine-tune the tamed microbes, she hopes for even better-tasting sake and cheese.

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