Data processing
Oral and gut microbiome compositional species and pathways data, serum metabolites and cytokines went through the same processing steps which included: (1) Log 10 transformation (2) Robust standardization using median and standard deviation calculated over 90% of the central distribution (3) Outliers clipping to five standard deviations from the mean (4) Features filtering out, if they existed in less than 20 samples (5) Missing values imputation with feature’s minimal value only if there was a value in participant’s complementary sample (pre- or post- intervention) (6) Batch correction if one of the first five principal components (PCs) explained at least 5% of the data’s variance and was significantly associated with a batch (