Comparative Analysis of Oral Microbiome

SPSS (IBM Corp. version 25.0) and PAST 3 [36 ] software packages were used for descriptive and inferential statistics. Group differences between continuous variables were tested using the Mann–Whitney U test, and categorical variables were tested using the chi-squared test. All tests were two-sided, and correction for multiple comparisons was conducted using the Benjamini–Hochberg false discovery rate (FDR). p-values were considered significant at FDR <0.05. Orthogonal partial least square discriminant analysis (OPLS-DA) (SIMCA 15; Sartorius Stedim Data Analytics AB, Malmö, Sweden) was used to search for differences in oral microbiota between the cases and controls. Clustering of subjects by bacterial taxa in the saliva microbiota was performed by agglomerative hierarchical cluster analysis using Ward’s method, and the linear discriminant analysis (LDA) effect size (LEfSe) method was used for high-dimensional class comparisons [37 (link)]. Potential molecular functions of the saliva microbiota were predicted using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) plugin for QIIME2 and converted to functions via the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology database (https://www.genome.jp/kegg/ko, accessed 1 September 2020) [38 (link)].