Transkingdom network analysis reveals the dominant role of ileal microbiota in host metabolism over colonic microbiota in diet-induced obesity.

Distinct gut habitats shape the spatial organization of resident microbes, with most studies focusing on the colon/feces and ileum as key sites for host-microbiota interactions. However, the relationship between microbial biogeography and host metabolism remains poorly understood. Here, we investigated the differential responses of ileal and colonic microbiota to a high-fat diet using two-way analysis of variance. Furthermore, we explored their respective contributions to diet-induced metabolic disorders through transkingdom network analysis (TkNA), a well-established causal-inference approach. A total of 39 taxa, including IMPORTANCE: Evidence shows that gut microbiota plays a crucial role in host metabolism, but its composition varies across intestinal segments. While the ileum is essential for nutrient absorption, the colon hosts a denser, more diverse microbiota involved in fiber fermentation. It remains unclear which segment has a greater impact on host metabolism. In this study, we used an advanced network analysis to integrate multi-omics data and perform causal inference. Compared to colonic microbiota, ileal microbiota showed stronger associations with liver gene expression, liver metabolites, serum metabolites, and host metabolic phenotypes. These findings suggest that the ileal microbiota has a more significant influence on host metabolism, highlighting its importance in future microbiota research.