Comparison of Bioinformatics Tools and Procedures for Food Processing Surface Microbiota Characterization Using 16S RNA Sequences

There is significant interest in sequencing of the 16S rRNA gene to provide greater insight into microbiota attributes on food processing surfaces. Bioinformatic pipelines are used to analyze and process sequencing data, and there has been significant debate of the advantages and disadvantages of different pipelines. Moreover, there is minimal guidance on pipeline selection for different types of microbiota. This research quantifies the impact of bioinformatics tools and procedures on samples collected from food processing surfaces. This study found that the ecological characterizations of food processing surface microbiota differed based on normalization and sequence aggregation method selection. Overall, this study provides new insight into procedures for analyzing uneven, low-density microbiomes.