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A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine1

Recent advances in molecular biotechnology have introduced an array of powerful techniques for studying the microbial ecology of beverage and food fermentations. Molecular tools such as denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, fluorescent in situ hybridization, clone libraries, and quantitative polymerase chain reaction are sensitive methods for microbial community analysis and have several advantages over traditional, culture-based techniques. Some of these tools have far-reaching benefits, not only for fermentation research but also for rapid quality-assurance applications in the beverage fermentation industry. Additionally, the increasing accessibility of next-generation sequencing technologies, such as Illumina and 454 Life Sciences sequencing platforms, is bringing some of these powerful new tools within reach of researchers for food or fermentation analysis. This promises high-resolution studies revealing deep community structure in fermentation and processing environments, endeavors with obvious benefits to understanding and controlling mixed microbial fermentation systems and process hygiene. This review presents an overview of the current technologies available for microbial community analysis and considers their specific application for fermentation research and industrial purposes, as well as providing an outlook on the future of community profiling in beer and wine.