Oral Microbiome Profiling Between Dietary Groups

Data from qPCR were processed in IBM SPSS Statistics for Windows v21 (IBM Corp., Armonk, NY) using the Mann–Whitney U-test to compare the concentrations of bacteria in the two diet groups. Fisher’s exact test was performed to determine if there was an association between diet group and low (<1,000 pg DNA/µL) or high (≥1,000 pg DNA/µL) concentrations of S. wiggsiae. Data from HOMINGS were processed by MeV v4.9 [19 (link)] and GraphPad Prism (GraphPad Software, Inc., La Jolla, CA) to calculate the Shannon diversity index (α-diversity). Data reduction and graphic presentation using principal component analysis and correspondence analysis were performed. Comparisons of the two diet groups at probe level were made using the Mann–Whitney U-test. An adjusted p-value of <0.05 was considered significant. Demographics of subjects with and without sufficient DNA in plaque samples were compared by Student’s t-test (age, sex, DMFT) and Mann–Whitney U-test (oral hygiene).
Sample size was based on results from a previous study analyzed with the same assays [20 (link),21]. It was estimated that approximately 30 subjects in each sugar category would be sufficient in order to avoid type I and type II errors.