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Abstract
In the last two decades major changes have occurred in how microbial ecologists study
microbial communities. Limitations associated with traditional culture-based methods
have pushed for the development of culture-independent techniques, which are primarily
based on the analysis of nucleic acids. These methods are now increasingly applied
in food microbiology as well. This review presents an overview of current community
profiling techniques with their (potential) applications in food and food-related
ecosystems. We critically assessed both the power and limitations of these techniques
and present recent advances in the field of food microbiology attained by their application.
It is unlikely that a single approach will be universally applicable for analyzing
microbial communities in unknown matrices. However, when screening samples for well-defined
species or functions, techniques such as DNA arrays and real-time PCR have the potential
to overtake current culture-based methods. Most importantly, molecular methods will
allow us to surpass our current culturing limitations, thus revealing the extent and
importance of the 'non-culturable' microbial flora that occurs in food matrices and
production.