Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

• Published in: Proceedings of the National Academy of Sciences - PNAS 2011-08, Vol.108 (35), p.14539-14544
• Main Authors: Libkind, Diego, Hittinger, Chris Todd, Valério, Elisabete, Gonçalves, Carla, Dover, Jim, Johnston, Mark, Gonçalves, Paula, Sampaio, José Paulo
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; animals; Bacteria; Base Sequence; Beverages; Biofuels; Biological Sciences; Biological taxonomies; Brewing; Classification; Crops; Demography; Domestication; Ecological genetics; Ecology; Fagus; Food; food production; Forests; Genetics; genome; Genomes; genomics; Human genetics; Hybridity; Hybrids; Livestock; livestock breeding; Metabolism; microbial ecology; Microbial genetics; Molecular Sequence Data; New species; Nothofagus; Nucleotide sequence; nucleotide sequences; Plant breeding; Plant domestication; Preservation; Saccharomyces; Saccharomyces bayanus; Saccharomyces carlsbergensis; Saccharomyces cerevisiae; Saccharomyces cerevisiae - classification; Saccharomyces cerevisiae - genetics; Saccharomyces pastorianus; Saccharomyces uvarum; Sugar; sugars; sulfite; Sympatry; Yeast; Yeasts
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1105430108

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.