Cell recovery and DNA extraction methods skew relative abundance estimations of foodborne pathogens and spoilage organisms on stainless steel surfaces.

Amplicon sequencing investigations of surface microbiota in food facilities often report the relative abundance of bacteria and fungi. However, physiological differences among cell types can result in variable cell recovery and DNA yields, thereby skewing relative abundance estimates. Here, we evaluated (i) variations in cell recovery among different bacterial and fungal species after surface swabbing and (ii) the impact of DNA extraction protocols on relative abundance estimates from artificially inoculated stainless steel surfaces. Our results showed that IMPORTANCE: Amplicon sequencing has been used to characterize microbial communities on facility surfaces. However, few studies have evaluated the accuracy of the amplicon sequencing workflow for quantifying spoilage and pathogenic organisms in these microbial communities. Here, we assessed the accuracy of amplicon sequencing to evaluate the relative abundance of spoilage and pathogenic organisms commonly found in food-processing environments. The results revealed biases in relative abundances due to limitations in cell recovery and DNA extraction methods. These findings revealed the potential biases in surface microbiota characterization in food facilities and the need to refine current recovery and extraction methods to enhance the accuracy of microbiota characterization.