A guild consists of microbes with diverse taxonomic backgrounds, but thriving or declining together, showing coabundance behavior. (i) Initial tagging and identification of individual microbial entities using ASVs or MAGs, each assigned a UUID for precise tracking. (ii) Analysis of interactions among microbial entities to identify patterns of coexistence and influence, revealing the foundational relationships within the microbiome. Clustering of microbes into guilds based on coabundance analysis, where members share ecological niches and exhibit similar abundance patterns across different conditions or samples. (iii) Emergence of complex microbial behaviors and functions from the interactions within and between guilds, highlighting the collective capabilities of the microbiome. Integration of guild activities into broader systems-level functions that affect host physiology and health, encapsulating the holistic effect of microbial interactions.