A multi-omic analysis delineates a causal protective role for Bifidobacteriaceae and implicates key host genes in inflammatory bowel disease

Background While gut microbiota dysbiosis is a hallmark of inflammatory bowel disease (IBD), the causal microbial drivers and their host-mediated mechanisms remain elusive. This study leverages an integrated multi-omics approach, combining Mendelian randomization (MR) and transcriptome analysis, to bridge the gap from microbial causality to host molecular pathways. Methods We performed a two-sample MR analysis using large-scale genome-wide association study (GWAS) data to identify specific gut microbiota taxa with a causal effect on IBD risk. Subsequently, we conducted a multi-level bioinformatic analysis of IBD patient transcriptomes to elucidate the downstream host genes, regulatory networks, and immune cell interactions modulated by these causal microbes. Results Our MR analysis established a robust causal protective effect of the family Bifidobacteriaceae against IBD. Integrating this finding with transcriptomic data, we identified three key host genes as potential mediators acting through distinct mechanisms: LCT , whose regulation may foster a protective prebiotic niche; MCM6 , which appears to function as a hub driving the proliferation of pathogenic immune infiltrates; and UBXN4 , a critical regulator of cellular proteostasis, the failure of which can precipitate inflammatory stress. Conclusions This study moves beyond association to delineate a causal protective role for Bifidobacteriaceae in IBD and pinpoints specific host genes ( LCT, MCM6, UBXN4 ) through which this effect is likely orchestrated. These findings provide a novel mechanistic framework for host-microbiota interactions and highlight new pathways for therapeutic intervention in IBD.