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).