Microorganisms and macroorganisms are routinely associated with interactions that shape contrasting environments between different host microbial communities {{59 Hughes-Martiny, JB 2006;}}. These interactions are dominated by microbes because microbes outnumber host cells by many orders of magnitude {{68 Savage, DC 1977;}} and provide metabolic functions absent in the host {{69 Gill, SR 2006;}}. Naturally occurring populations may also include host-pathogen colonization interactions {{16 Critzer, FJ 2010;}} or health and disease states{{20 Frank, DN 2007; 21 Ley, RE 2005;}}. Interactions may elude the importance of the symbiotic or mutualistic relationship in community structure {{22 Ley, RE 2008; 40 Walter, J. 2010; 38 Oh, PL 2010; 39 Frese, SA 2011;}}.Ecosystems, including engineered ones, are complex systems in which microorganisms are found in heterogeneous communities. Their behavior in the environment is often unknown due to the lack of adequate detection and identification techniques. There has long been a need to more accurately evaluate microbial ecosystems {{70 Stahl, DA 1988;}}. Historically, microbial ecology was reductive and relied solely on the ability of microbes to be cultured, analyzed, and enumerated {{10 Mack, WN 1977;}}; Microbes that met this criterion were thought to comprise the dominant members of the environments from which they were isolated, however most environments are dominated by uncultured microorganisms. In some environments it is estimated that as many as 99% of endogenous species are uncultivable with existing methodologies {{74 Amann, RI 1995;}}. This means that any investigation of microbial community members relies exclusively on culture-based techniques such as plate counts or... middle of paper... ant bacteria including spinach and fecal isolates. However, if rare species are more important in detecting differences between healthy and contaminated foods, much more in-depth characterization of the microbiome may be needed.20 Community profiling through massively parallel sequencing is still time-consuming and highly technical, so it is limited to laboratory settings. To implement risk management techniques, sequencing candidates with a high risk of fecal contamination will need to be analyzed by other methods. Quantitative real-time PCR is an interesting application for this as it allows 96 different reactions to be completed simultaneously in just a few hours. If high-risk microbial candidates could be identified and established, future work would focus on implementing alternative methods that could be used in the food industry.