Purpose: The purpose of this study was to evaluate NGS based 16S rRNA sequences as a tool to assess microbial flora of raw tomatoes and tomato products.
Methods: Raw tomatoes were sampled from three different lots over a two-month period and tested for APC by pour plating methods. Three different lots of raw processed products, including diced tomatoes, diced tomatoes with chilies, and tomato paste, were also collected and tested for APC. All samples collected were subjected to total DNA extraction, PCR amplification using universal 16S rRNA primers, and sequenced on NGS platform using metagenomics workflow. Taxonomy at genus level was assigned for each sample against the Greengenes Database.
Results: The average APC of raw tomatoes for three lots was 7.33 ± 0.52 logs CFU/gram. The average APC for diced tomatoes, diced tomatoes with chilies, and tomato paste was 6.01 ± 0.63, 6.89 ± 0.60, and 4.89 ± 0.92 logs CFU/gram, respectively. The 16S rRNA sequences showed consistency of microbial flora for the same type of products among three different lots tested. These results also show that raw tomatoes had the most microbial diversity and many microbial populations were reduced or eliminated after the process of tomatoes into paste (before the heating step) even though only a 2 log APC reduction was observed. However, not many microbial population changes were observed among raw tomatoes, diced tomatoes, and diced tomatoes with chilies (before the heating step). The alterations in the microbial populations are likely due to differences in processing between the paste and diced products.
Significance: These data suggest NGS based 16S rRNA sequencing may be a useful tool for the assessment of microbial diversity of food products and these data may eventually be useful to evaluate processing parameters specific to different product types and desired quality attributes.