MINERVA-microbiome network research and visualization atlas: a scalable knowledge graph for mapping microbiome-disease associations

Abstract

Bacterial pathogens contribute significantly to the global burden of disease. Understanding their complex interactions with human health is essential for developing new diagnostic, preventative, and therapeutic strategies. While recent breakthroughs have revolutionized our understanding of these relationships, the rapid expansion of microbiome research presents a significant challenge: knowledge remains scattered across scientific literature, hindering comprehensive analysis and clinical translation. To address this, we introduce MINERVA (Microbiome Network Research and Visualization Atlas), an innovative platform that leverages a fine-tuned large language model to systematically map microbe-disease associations across extensive scientific literature. MINERVA constructs a rich, ontology-driven knowledge graph that prioritizes accuracy and transparency, enabling efficient exploration and discovery of previously hidden associations relevant to clinical decision-making. The platform features specialized modules that allow researchers to analyze individual microbes and diseases, visualize complex relationships within the knowledge network, uncover hidden connections through advanced graph algorithms and machine-learning models, and perform personalized and population-level microbiome compositional analysis. These capabilities facilitate the identification of disease risks, comorbidities, and actionable insights, supporting both research and clinical decision-making. By bridging the gap between microbiome research and real-world applications, MINERVA has the potential to transform our understanding of microbe-disease interactions, accelerating discoveries and advancing patient care. The MINERVA platform is available at https://minervabio.org/.