Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures

The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.