Micro- and macro-organisms are usually associated with interactions shaping contrasting environments between different host microbial communities {{59 Hughes-Martiny, JB 2006;}}. These interactions are dominated by microbes, because microbes outnumber host cells by several orders of magnitude {{68 Savage, DC 1977;}} and provide metabolic functions that the host lacks {{69 Gill, SR 2006 ;}}. Natural populations may also include interactions between host-pathogen colonization {{16 Critzer, FJ 2010;}} or health and disease states{{20 Frank, DN 2007; 21 Ley, RE 2005;}}. Interactions can elude the importance of symbiotic or mutualistic relationships in community structure {{22 Ley, RE 2008; 40 Walter, J. 2010; 38 Ah, PL 2010; 39 Frese, SA 2011 ;}}. Ecosystems, including artificial ones, are complex systems in which microorganisms occur in heterogeneous communities. Their behavior in the environment is often unknown due to the lack of appropriate detection and identification techniques. There has long been a need to more precisely assess 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 meeting this criterion were thought to be the dominant members of the environments in which they were isolated, but most environments are dominated by uncultured microorganisms. In some environments, it is estimated that up to 99% of endogenous species are uncultivable with existing methodologies {{74 Amann, RI 1995;}}. This means that any survey of members of the microbial community relies solely on culture-based techniques such as plate counting 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 deeper characterization of the microbiome may be necessary.20 Community profiling by massively parallel sequencing is still time-consuming and highly technical and is therefore limited to laboratory parameters. To implement risk management techniques, candidates from sequencing relating to a high risk of fecal contamination will need to be analyzed by other methods. Real-time quantitative PCR is an interesting application as it allows 96 different reactions to be carried out simultaneously in a few hours. If high-risk microbial candidates can be identified and established, future work will focus on implementing alternative methods that could be used in the food industry..