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.
