Although the food industry, authorities, and legislation tend to focus on surveillance and control of pathogenic bacteria, the majority of bacteria in the food processing environment are, in fact, non-pathogenic. These bacteria, which can be isolated on non-selective growth media are often referred to as the natural flora, total bacterial count, heterotrophic plate count, aerobic plate count, etc.; and, for the majority of food industries, the identity of these microorganisms is unknown. There is a number of reasons for increased attention to the residential, non-pathogenic bacteria in the food production environment. Obviously, they may pose a threat for the food quality. Secondly, several studies imply that the fate of pathogens introduced into the processing environment may be affected by the non-pathogenic bacteria present. Also, for other ecological niches, it has been speculated that residential bacteria could play a role in the persistence and spread of antimicrobial resistance genes.   Recently, the introduction of sequence based microbiota analyses have given new insight into the identity of microorganisms on surfaces in the food industry. This methodology provides high throughput and in depth identification compared to cultivation based techniques; and, its use provides new insights into the microbial ecology of processing environments, as well as contamination routes for spoilage bacteria.

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