MicrobiomeKG: Bridging Microbiome Research and Host Health Through Knowledge Graphs

Skye L Goetz¹Amy K Glen²Gwênlyn Glusman^1*

• ¹Institute for Systems Biology (ISB), Seattle, United States
• ²Oregon State University, Corvallis, Oregon, United States

The microbiome represents a complex community of trillions of microorganisms residing in various body parts, and plays critical roles in maintaining host health and well-being. Understanding the interactions between microbiota and host offers valuable insights into potential strategies to promote health, including microbiome-targeted interventions. We have created MicrobiomeKG, a Knowledge Graph for microbiome research, bridging various taxa and microbial pathways with host health. This novel knowledge graph derives algorithmically-generated knowledge assertions from the supplementary tables supporting published microbiome papers. By identifying knowledge assertions from supplementary tables, and expressing them as knowledge graphs, we are casting this valuable content into a format that is ideal for hypothesis generation. To address the high heterogeneity of study contexts, methodologies, and reporting standards, we leveraged neural networks to implement a standardized edge scoring system, which we use to perform centrality analyses. We present three example use cases, linking helminth infections with non-alcoholic fatty-liver disease via microbial taxa, exploring connections between the Alistipes genus and inflammation, and identifying the Bifidobacterium genus as the most central connection with Attention Deficit Hyperactivity Disorder. MicrobiomeKG is deployed for integrative analysis and hypothesis generation, both programmatically and via the Biomedical Data Translator ecosystem. By bridging data gaps and facilitating the discovery of new biological relationships, MicrobiomeKG will help advance personalized medicine through a deeper understanding of the microbial contributions to human health and disease mechanisms.