Using eDNA methodologies to identify the presence/absence of S. thermophilus in yogurt products

Abstract

AbstractThe advent of low-cost nuclear acid extraction allows for the creation of low-cost assays which can specifically be used to determine the presence or absence of bacteria in a variety of environments. Commercially sold dietary yogurt claims to contain bacteria forming a microbiome which has been previously linked to improved health outcomes in incidence rates of type 2 diabetes in vulnerable populations. The predicted outcome was that a main bacterial culture used in yogurt production (S. thermophilus) would be present and would be detectable using eDNA methodologies since it is fundamental to the making of yogurt. We gathered DNA from yogurt using yogurt dilutions and filter paper; we then extracted the DNA and also sequenced and used PCR to amplify the DNA. We sequenced PCR products to verify their identity through processing with publicly available BLAST tools which reference already accessioned bacterial genomes. Yogurt from four different commercially available brands (in the U.S.) was tested; not all yogurts tested positive for the bacteria, with higher concentrations of the bacteria in imported Greek-style yogurts, lower concentrations in domestically produced Greek-style yogurts, and no bacterial DNA detected in domestically produced ‘regular’ yogurt products. This research suggests that not all yogurts are equal, putting into question the whole-sale claims made on dietary yogurt’s probiotic preventative health effects and calling for a more detailed analysis to determine firm causal links between the microbiota of yogurts and preventative health effects.