Core microbes are ecological generalists supporting the host and ecosystem functionality and stability

Core gut microbes persist across diverse gut ecosystems, raising the central question in microbiome research of what defines core microbes and the factors driving their persistence across hosts? Using the rumen microbiome as a model system, our study reveals that core microbes exhibit distinct attributes of ecological generalists, including greater strain variability and broader functional capacity, linked to larger genome sizes. These traits enable core microbes to be metabolically independent while also supporting non-core microbes and the host. Core taxa produce essential metabolites, such as amino acids and vitamins, and encode fiber-degrading enzymes crucial for host nutrition. Additionally, they engage in cross-feeding, providing non-core microbes with vital nutrients. This independence positions core microbes as foundational pillars of gut ecosystem stability. Our findings offer valuable insights into the functional essence of core microbes, with implications that extend beyond ecology to microbiome-based interventions in food security and environmental sustainability.