Co-occurrence network of VMB
ASVs present in less than 10% of samples were excluded from the network analysis. Significant correlations between the relative abundance of ASVs were evaluated using Sparse Correlations for compositional data algorithm implemented in the SparCC python module (Friedman and Alm, 2012), while the corresponding networks were plotted using the R package, ‘igraph’. Only correlations with an absolute correlation greater than 0.15 and an adjusted p-value of less than 0.05 were plotted.
Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis
ASVs with a relative abundance much more than 0.001% were included and high abundance ASV taxonomy was mapped based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using the R package, ‘Tax4Fun;. The Wilcoxon test was performed to detect biomarkers of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that differed significantly between the PCOS group and the control group (FDR<0.25).