BileActome reveals community-assembled bile acid metabolism in the rumen microbiome

Microbial bile acid metabolism is an important link between microbiomes and host physiology, but its genetic basis remains difficult to resolve from genome and metagenome data. This is largely because existing annotation resources are not designed for the high sequence diversity and functional complexity of microbial bile acid genes. Here we present BileActome, a reusable annotation resource developed specifically for microbial bile acid metabolism. BileActome defines 27 experimentally supported gene families, including bile salt hydrolases, bile acid-inducible operon genes, and microbial hydroxysteroid dehydrogenases. Its design prioritizes experimentally supported functional sites when available and conserved domain features otherwise, while also distinguishing key functional subtypes. We applied BileActome to 1693 high-quality rumen metagenome-assembled and isolate genomes and validated its performance using controlled in vitro rumen fermentations under three bile acid interventions. In metagenomic gene-catalog analyses, BileActome enabled pathway-level interpretation of microbial responses to bile acid exposure, with the most reproducible responses centered on Bai-associated gene families. At genome scale, it generated a phylogeny-informed map of bile acid metabolic potential that was broader and more informative than Kyoto Encyclopedia of Genes and Genomes (KEGG)-based annotation. Further analyses of genomes, local gene organization, and genome-level guilds showed that bile acid metabolism in the rumen is modular, phylogenetically structured, and distributed across different microbial members. Deconjugation and oxidation/epimerization-related functions were widespread, whereas complete bile acid-inducible systems were less common. Together, these findings support a community-assembled model of bile acid metabolism and establish BileActome as an open and reproducible framework for studying specialized microbial functions in complex ecosystems.