Genomic Profiling of Microbial and Functional Diversity during Pulque Fermentation

Domestication refers to the genetic modification of a species by breeding it in isolation from its ancestral population in an effort to enhance its utility to humans. The domestication of plants and livestock ~10,000 years ago was one of the most significant events in human history as it led to the rise of civilizations, the establishment of government, technological innovations, and an abundant food surplus. The origins, genetic targets, and functional effects of domestication have been extensively studied in domesticated crops, livestock, and pets. However, molds, yeasts, and bacteria were domesticated in parallel with plants and animals, but remain understudied despite their role in the preservation, quality, consistency, and flavor of traditionally fermented foods and beverages. Zymomonas mobilis is an ethanol-producing bacterial species involved in the production of pulque, a 4,000 year old traditional Mexican fermented beverage made from agave sap (aguamiel). Phylogenomic analysis of Z. mobilis revealed that pulque-derived isolates are monophyletic, providing support for a domesticated lineage. Metagenomics analysis showed a rapid increase of Z. mobilis during the fermentation process and a highest abundance in the last stage of the fermentation process (pulque) compared to other microbes associate with this environment. We hypothesize that the long-term continual passage of Z. mobilis in the pulque has led to adaptation to food environment. Here, we seek to understand the evolutionary processes, genetic modifications, and phenotypic adaptations that underlie the effect of domestication on pulque derived isolates of Z. mobilis.