Wild yeast have more complex genes: See also wild yeast ferments.

‘The story of yeast: Domesticated tipple,’ The Economist 10th Sept 2016, p.69

Cattle ranchers know that if they want to increase their yields it is best to breed their largest cows with their biggest bulls. Microorganisms can also be bred selectively. Given that yeasts have a long history of being used to ferment food and drink, archaeologists have argued for years that early craftsmen may have selectively bred yeast strains without even realising it.

Now there is evidence to support this idea. Steven Maere of the University of Ghent and Kevin Verstrepen of the University of Leuven, both in Belgium, and their colleagues have been studying the genomes of culinary yeast species. As they report in Cell this week, the researchers have found evidence that people started domesticating yeast strains, particularly those used in beer, some 500 years ago.

Today’s bakers, vintners and brewers have intimate knowledge of yeasts and choose strains that improve their products and grant specific flavours. But until the work of Louis Pasteur in the mid-19th century nobody knew that microorganisms existed. However, a process called “backslopping”, whereby part of an old successful mix of fermented dough, wine or beer is seeded into a new mix, might have allowed early yeast users to confine species that had favourable characteristics in man-made environments for years on end, effectively domesticating them. Drs Maere and Verstrepen suspected that regular backslopping would have resulted in yeasts developing traits that led them to thrive in environments managed by humans, but to struggle in the wild. To explore that idea, they set up an experiment.

Working with a team of experts from White Labs, a company in San Diego that develops and sells yeasts, the researchers analysed the genomes of 157 strains of Saccharomyces cerevisiae, a yeast species that is commonly used today. Most were beer strains but the team included a number of wine, spirit, sake and bread yeasts for comparison. They knew from past studies that it was common for organisms exposed to artificial selection to carry evidence of such tinkering in the form of duplicate chromosomes and genes. And, sure enough, they found these characteristics in abundance and noticed that all the strains seemed to stem from wild ancestors that lived 500 years ago.

Further support came from traits carried by their genes. All yeasts engage in asexual reproduction most of the time. But wild species are capable of mating when genetic diversity in a population declines. Such a trait can prevent populations from becoming homogenous and thus vulnerable to a single disease or predator, but it serves no purpose in populations living in stable, protected man-made environments and ought thus to fade away. This is precisely what the researchers found. More than 40% of the beer yeasts were found to be incapable of reproducing sexually, and the others showed dramatically reduced sexual fertility.

Although domestication led sexual reproduction to decay, traits useful for life in a brewery became more common. The researchers found that genes involved in the fermentation of maltose, the main sugar found in beer, were duplicated several times, allowing beer yeasts to complete the fermentation process more rapidly than their feral ancestors. Similarly, wild yeasts typically carry genes associated with a range of unpleasant flavours; and these genes were rare in the culinary ones. Intriguingly, all these signs of domestication were far stronger in the 102 brewing strains that the researchers studied than those in the wine strains.

The evidence suggests that yeast domestication began in the 1500s and was more pronounced in brewing than it was in winemaking. Drs Maere and Verstrepen suggest that this may be down to different practices. Brewing yeasts were likely to breed continuously in a man-made environment, since they are recycled after each fermentation batch and beer is produced all year. In contrast, wine yeasts are only grown for a short period every year, and spend much of their lives in and around vineyards where they are subject to intermingling with wild strains, so are subjected to natural selective pressures.

The work was more than an academic exercise. The researchers went on to select a strain of beer yeast that shows very efficient fermentation, but also produces an unwanted spicy flavour, and crossed it with a less efficient but better-smelling sake strain. By selecting progeny without the gene variants for the off-flavour, they obtained a new beer yeast that combines swift fermentation with a lovely, fruity aroma. And this could be just the beginning. The scientists expect a range of novel yeast hybrids to follow from their research.