Saccharomyces cerevisiae as the first domesticated microbe
While these adaptations, presumably to the presence of fruit-bearing plants occurred millions of years prior, as described above, new opportunities arose for Saccharomyces yeasts relatively more recently (approximately 8,000-10,000 years ago). Humankind abandoned its hunter-gatherer lifestyle and introduced a horticultural tradition during the Neolithic evolution. After that, it did not take long before people realized that exposing fruits and grains to the environment (sometimes) positively changed the characteristics of these products significantly, and additionally prolonged their shelf life. From then on, beer and other fermented beverages such as wine, sake, cider or mead were an inherent part of the human diet, as they served as a source of nutrition, as medicine, and as a vital supply of uncontaminated water (Gibson and Liti, 2014; Hornsey, 2003; Kodama et al., 2006; Libkind et al., 2011). Later, skilled artisans found out that it paid to keep a small sample of fermented dough or beer sediment and mix this sample with a new, unfermented batch. In this way, without realizing it, they transferred specific, well-adapted microbes from one fermentation cycle to the next, thereby introducing the concept of starter cultures. During these consecutive fermentation steps, several novel superior yeast mutants and variants emerged through (mainly unintentional) artificial selection by breeding and directed evolution. It is now hypothesized that this practice induced the gradual adaptation of Saccharomyces yeasts to man-made conditions, resulting in organisms specialized in specific fermentation environments but behaving suboptimal in most other, more ‘natural' habitats, thereby making S. cerevisiae one of the oldest domesticated organisms on the planet (Fay and Benavides, 2005; Liti et al., 2009; Sicard and Legras, 2011).
Although these initial steps in microbial domestication happened haphazardly and are rarely documented, genetic analysis of current biodiversity enables the identification of specific adaptation. Not unexpectedly, these characteristics are often unique for specific types of industrial fermentation processes, e.g. brewing, baking, and winemaking (Borneman et al., 2011; Sicard and Legras, 2011; Spor et al., 2009; Will et al., 2010) (Table 6.2). However, it is important to note that some of these trait dissimilarities might be due rather to genetic drift and in fact pre-date or coincide with the emergence of synthetic fermentation environments (as suggested in Warringer et al., 2011).