Revealing the interactions between microbes, metabolites, and dietary compounds based on microbial genomes

The role of the gut microbiome in predicting response to diet and developing personalized dietary recommendations has been increasingly recognized. Yet, microbiome-based dietary recommendations depend on whether gut microbes have the metabolic capacity to utilize the dietary compounds and then produce health-beneficial metabolites. A systematic assessment of the metabolic capacity of gut microbes is still lacking. In this study, we leveraged the metabolic networks constructed from well-annotated microbial genomes to characterize the potential interactions between microbes and metabolites, specifically emphasizing the interactions between microbes and dietary compounds. We revealed a substantial variation in the number of metabolites or dietary compounds in the microbial metabolic networks across different genera and a high metabolic similarity within the same genus. Furthermore, we observed a positive correlation between species' genome sizes and the number of metabolites or dietary compounds present in their metabolic networks. In addition, the number of species that can utilize a metabolite or dietary compound drastically varies, with some being used by a wide range of species and others only specialized by a few. Moreover, we proposed a new way to identify the dietary compounds that are specific to no more than ten species, and we validated the possibility of using one dietary compound and its linked bacteria to design synbiotics. Finally, we observed that metabolically similar microbial taxa tend to have positively correlated abundances. These findings offer valuable insights crucial for designing microbiome-based dietary recommendations and understanding microbial interactions.