IMicAP: an intelligent microbial application platform for knowledge-driven microbiome research

Background Microorganisms play a pivotal role in health and disease, yet microbial research is hindered by fragmented data, heterogeneous knowledge representation, and a lack of integrated analytical tools. Existing databases and knowledge graphs often focus narrowly on genomic information, leaving critical metabolomic and literature-based associations underdeveloped. Results We developed the Intelligent Microbial Application Platform (IMicAP), an AI-driven, open-access web platform that integrates 12 microbial databases and over 35 million articles. IMicAP delivers 5 core modules: (1) Knowledge Query module for rapid data retrieval; (2) Knowledge Graph module for multi-hop reasoning and hypothesis generation; (3) Intelligent Question-Answering module for professional natural language dialogue in the field of microbiology; (4) Genome Browser module for genomic visualization; and (5) 16S rRNA Sequencing Analysis module for zero-code microbial bioinformatics analysis. Using curated microbe-disease and microbe-small molecule relations extracted with biomedical language models, IMicAP enables context-aware exploration of microbial relations. Conclusion IMicAP (available at: https://www.imicap.com:8443 ) is the first comprehensive, open-access, AI-powered microbial platform designed to bridge the gap between fragmented microbial data and actionable biological insights. It directly addresses 4 key limitations in existing resources: (1) Fragmented analysis without integrated workflows; (2) Narrow disease scope covering only one or two disease types; (3) Incomplete knowledge from restricted data sources; and (4) neglect of metabolomic information. IMicAP serves as a versatile resource for advancing microbiome research and translational discoveries. Future development focus on expanding microbial coverage, enhancing reasoning scalability, and evolving toward a dual knowledge-and-data-driven architecture to further support mechanistic discovery in microbial systems biology.