Fig. 6

General overview of transcriptomics and metabolomics integration workflow. It begins with sample preparation where interacting microbes are cultured and processed to ensure the high quality for analysis. In the metabolomics phase, metabolites are extracted and quantified using LC–MS techniques. The data is then processed and subjected to rigorous analysis to identify significant metabolite changes and pathways. Concurrently, in the transcriptomics analysis, mRNA is extracted from the same samples and converted into cDNA libraries, which are then sequenced using next-generation sequencing technologies to generate data that will be processed and allow for the determination of gene expression profiles. The data from metabolomics and transcriptomics analyses are integrated, enabling researchers to comprehensively understand molecular changes within the biological system