My lab was among the first to use modern high throughput microbial ecology tools to characterize food and beverage fermentations and facilities. This approach represents a paradigm shift in how we can analyze microbial biogeography within food or beverage production systems. With these approaches we seek to accurately map microbial flow throughout the process environment, identifying key environmental parameters that drive distribution of taxa—both beneficial and detrimental—to food and beverage product quality.

Sample publications from this area:

• Liu, J., Y. Zhu, M. Jay-Russell, D. G. Lemay and D. A. Mills.  2020.  Reservoirs of antimicrobial resistance genes in retail raw milk.  Microbiome 8:99. PMC7320593.
• Bokulich, N. A., C. Masarweh, T. S. Collins, G. Allen, H. Heymann, S. E. Ebeler and D. A. Mills. 2016. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio 7:e00631-16. PMC4959672.
• Bokulich, N. A., J. Bergsveinson, B. Ziola, D. A. Mills. 2015. Mapping microbial ecosystems and spoilage-gene flow in brewery environments highlights patterns of contamination and resistance. Elife 4:e04634. PMC4352708.
• Bokulich, N. A., J. H. Thorngate, P. M. Richardson and D. A. Mills. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.  Proceedings of the National Academy of Sciences 111:E139-148. PMC3890796.
• Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, J. G. Caporaso.  2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10:57-59. PMC3531572.