2.10. Statistical Analysis
Depression, Insomnia, HRSD
TSS
To compare baseline characteristics of patients, we utilized either the Wilcoxon test or Fisher test. To evaluate differences between treatment groups (Placebo versus Probiotic) concerning changes in clinical response variables from baseline to the end of the intervention, including Beck Depression Inventory (BDI), Hamilton Psychiatric Rating Scale for Depression (HRSD), Insomnia scale, and Diet Quality Index—International (DQI-I), we employed a mixed-effect linear model implemented in the lme4 R package (version 1.1–34) [The analysis of gut microbiome data was conducted at baseline, where alpha-diversity measures were compared between groups using a mixed-effect model (as described above), considering the type of surgery. To test for significant differences in the composition of biological communities among groups, we applied Permutational Multivariate Analysis of Variance (PERMANOVA) implemented in the vegan R package (2.6-4) using the Bray–Curtis dissimilarity metric. Principal Coordinate Analysis (PCoA) was used for reducing the dimensionality of beta-diversity and representing it in two-dimensions.In the analysis of genus-level data (with a 10% prevalence filtering), differential abundance analysis (DAA) was performed using five different methods: ALDEx2, ANCOMBC2, WilcoxTSS, WilcoxRarefied, and LEfSe. WilcoxTSS and WilcoxRarefied applied the Wilcoxon test to relative abundance data (TSS, total sum scaling) and rarefied data WilcoxRarefied (with sampling depth = 14,193), respectively. All statistical analyses were carried out using the R software (version 4.2.3, R Core Team (2022)) [