Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function
Omar E. Tovar-Herrera, Ido Grinshpan, Gil Sorek, Ido Lybovits, Liron Levin, Sarah Moraïs, Itzhak Mizrahi
Abstract
Some microbes persist across diverse gut microbiomes, raising the question of what features define these core taxa and allow them to persist across hosts. Using the rumen microbiome as a model system, we show that core microbes exhibit distinct attributes of ecological generalists, including greater strain variability and broader functional capacity, linked to larger genome sizes. By analysing ~3,000 genomes of core and non-core microbes and metabolically measuring their functional attributes with both biochemical assays and untargeted/targeted metabolomics, we find that 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 fibre-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, and influencing these microbes could modulate microbiome functionality and ruminant host metabolism, with possible downstream consequences for food security and environmental sustainability. This study uses the rumen gut microbiome to show that core microbes exhibit attributes of ecological generalists with broad functional capacity and traits that enable them to be metabolically independent while also supporting non-core microbes and the host.