The burst of flavor from the first sweet corn of the summer and the proud stance of a show dog testify to the power of domestication. But also the microbial alchemy that turns milk into cheese, grain into bread and soy into miso. Like the ancestors of corn and dog, the fungi and bacteria that cause these transformations have been modified for human use. And their genomes have acquired many of the classic signs of domestication, researchers said in two conversations this month at a meeting in Washington, DC
Microbes cannot be “grown” in the normal sense because, unlike peas or pigs, individual microbes with the desired traits cannot be selected and mated. But people can grow microbes and choose the options that best serve our purposes. Studies show that the process, repeated over thousands of years, has left genetic traits similar to those in domestic plants and animals: microbes have lost genes, evolved into new species or strains, and become unable to thrive in the wild.
Research “reaches the mechanisms” of how microbial domestication works, says Benjamin Wolfe, a microbiologist at Tufts University. By revealing which genes are key to microbial valuable traits – and which can be lost – the work can help further improve the organisms that make up much of our food and drink, “especially [with] growing interest in fermented foods, “said microbial ecologist Arian Peralta of the University of East Carolina.
Yeast used in bread making has long been considered domesticated because it has 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, ”said Vincent Somerville, a graduate student at the University of Lausanne.
Somerville and John Gibbons, a genomic at the University of Massachusetts, Amherst, independently focused on food fermentation, which helped early farmers and pastors transform fresh produce and milk into products that could last months or years. Gibbons took a closer look at the genome of Aspergillus oryzaethe mushroom that started the production of rice sake and soy sauce and soy miso.
When farmers are cultivated A. oryzae, the fungus – a eukaryotic whose DNA is enclosed in a nucleus – reproduces itself. But when people take some ready-made sake and transfer it to rice porridge to start fermentation again, they also transfer the cells to the fungal strains that developed and survived best during the first round of fermentation.
Gibbons compares the genomes of dozens A. oryzae strains with those of their wild ancestor, A. flavus. Over time, he found, the selection of people increased A. oryzaeits ability to break down starches and tolerate fermented alcohol. “Restructuring the metabolism seems to be a hallmark of domestication of fungi,” he told Microbe 2022, the annual meeting of the American Society of Microbiology, last week. For example, domesticated Aspergillus strains can have up to five times more copies of a starch metabolizing gene as their ancestor – “a brilliant way for evolution to increase this enzyme,” Wolfe said.
The genes of the domesticated A. oryzae also show small variations, and the genome has lost some key genes, including those for toxins that would kill the yeast needed to complete fermentation – and that can make people sick. The domestication has obviously been done A.oryzae more human-friendly, just as it cultivates bitter tastes from many food plants.
Somerville announced at the meeting that he had seen almost the same pattern in prokaryotes or nuclei-free organisms, including the bacteria used to make cheese. Early cheese producers created “starter” bacterial cultures that people in Switzerland used to make Gruyère and other cheeses. Since the 1970s, cheese producers have been collecting 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 job was having samples over time,” Wolfe said. “You can see the shaping of diversity,” as changes over the past 50 years allude to the trajectory of change in recent centuries.
All samples had low genetic diversity, with only a few strains of the two dominant species, Somerville reported. These few resistant strains are probably important for cheese quality, Gibbons said. Cultures have also lost genes from the 1970s, including some needed to produce certain amino acids that are needed to assemble proteins. But amino acids are expensive to produce – and these microbes live in milk, which is rich in protein. “They were able to release a bunch of genes they didn’t need,” Wolfe said. Somerville also discovered extensive gene exchange between microbes, one of the ways to acquire new genes.
Combining the studies, Gibbons concluded that the genomes of “domestic prokaryotes and microbial eukaryotes are very similar” to each other and to multicellular domesticated organisms. Peralta warns that the analogy with crops and animals is not perfect. Microbes can grow much faster and so can be “rediscovered” more easily. However, while researchers are fine-tuning the domesticated microbes, she hopes for an even better taste of sake and cheese.