Comparative Genomic and Functional Profiling of ECM-Associated Enzymes in Bacteroides, a Key Genus of the Human Gut Microbiome

Purpose The human extracellular matrix (ECM) provides essential cues for intestinal homeostasis. While most studies focus on ECM degradation by host cells, emerging evidence suggests that commensal gut bacteria may also contribute to these remodeling processes. Here, we systematically characterize the genomic diversity and functional activity of ECM-associated enzymes across Bacteroides, a dominant and metabolically versatile genus of the human gut microbiome. Methods We performed comparative genomic analyses across 11 Bacteroides species to identify putative genes encoding ECM-associated proteases and carbohydrate-active enzymes (CAZymes) and characterize their predicted substrate associations. Functional characterization included in vitro degradation assays using purified ECM substrates, complementary minimal media growth assays, and protease inhibition experiments to identify the major catalytic classes contributing to ECM protein degradation. Results Genes encoding ECM-associated CAZymes and proteases were identified across all 11 Bacteroides genomes, revealing widespread genomic potential for ECM degradation and considerable diversity in predicted substrate associations. Functional assays similarly revealed diverse ECM degradation profiles across species and substrates. Comparative genomic and functional analyses showed limited correspondence between substrate-associated gene counts and experimentally measured degradation phenotypes. Finally, protease inhibition experiments identified metalloproteases and serine proteases as the primary contributors to collagen and elastin degradation. Conclusions Our findings establish extracellular matrix degradation as a widespread functional capability of the Bacteroides genus and highlight the need to consider gut bacteria as potential modulators of host ECM remodeling and tissue homeostasis.