Influence of sampling and DNA extraction on 16S rRNA gene amplicon sequencing - Comparison of the bacterial community between two food processing plants

Some operational taxonomic units (OTUs) occurred predominantly in one of the companies, but none of them generated a clear hypothesis why one of the plants had recurrent contamination with L. monocytogenes. This work provides insights into the microbiomes of the two dairy companies but advises cautions in over-interpreting sequencing results as selective DNA extraction and sampling only reflect components of prevalent bacterial communities.