Gi-MAPS: a quantitative engineering framework for AI-guided pediatric gut microbiome ecological interpretation and digital-twin simulation

Background Quantitative and reproducible microbiome analysis is limited by fragmented workflows lacking standardized anaerobic sampling, absolute quantification methods, and transparent AI inference. Patent-documented engineering integration is required for reliable microbiome analytics at population scale. Methods Gi-MAPS was designed as an end-to-end analytical system integrating several core patented innovations, including (i) a press-activated anaerobic sample-preservation device that maintains ultra-low residual oxygen to protect obligate anaerobes during transport, (ii) a multiplex qPCR assay enabling simultaneous absolute quantification of key HMO-utilizing Bifidobacterium species in a single reaction, and (iii) a CIT-Net–based digital-twin engine that supports forward simulation of gut microbiota ecological trajectories. These modules are coupled with explainable ensemble artificial intelligence models to form a fully quantitative and simulation-enabled microbiome analysis framework. Each subsystem was validated under granted patents to define engineering performance boundaries and reproducibility specifications. Results System validation demonstrated <0.1% residual oxygen stability for anaerobic preservation, detection sensitivity down to five genomic copies per microliter, AUC > 0.97 for ecological maturity estimation, 89% accuracy for disease-risk classification, and 95% concordance for digital-twin forecasting. Execution-layer software copyright modules and filed patents extend automation, visualization, and future application domains. Conclusion Gi-MAPS provides a patent-anchored, standardized engineering framework whose key novelties lie in oxygen-controlled anaerobic sampling, absolute microbial quantification via multiplex qPCR, and digital-twin ecological simulation, enabling quantitative, function-aware, and prospective microbiome analysis. It establishes a reproducible foundation enabling large-scale cohort deployment, longitudinal ecological monitoring, digital-twin simulation, and future multi-omics integration.