For the KOs, Transcripts Per Kilobase Million (TPM) were calculated in R, accounting for sequencing depth per sample and gene lengths. Pathways from the significant KOs were obtained via the KEGGREST package in R, see the GitLab repository for details . To provide a comprehensive overview, TPM values of KOs sharing the same pathway were summed and ANOVA was performed to identify the statistically significant pathways across groups.