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Author ORCID Identifier


Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Molecular and Cellular Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

John G. Gibbons

Second Advisor

Ana Caicedo

Third Advisor

Li-Jun Ma

Fourth Advisor

Jeffrey Blanchard

Subject Categories

Bioinformatics | Biology | Food Science | Genomics


Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very stable compared to a wild environment, microbial dynamics are variable and fluctuating in terms of function diversity and abundance. Additionally, the process of backslopping, the constant transfer of previous fermented material to new batches could led to microbial specialization to human-made environment causing microbes to undergo domestication where adapted lineages are genetically differentiated from wild species. The goal of my dissertation was to understand and evaluate genomic and functional changes in fermenting food microbes and understand the impact of selection in domesticated microbes.


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.