AI-guided computational design of synthetic microbiota for next-generation immunomodulatory applications

The growing recognition of the human microbiome as a key regulator of immune homeostasis has accelerated the application of computational intelligence for microbiome-driven disease understanding and therapeutic design. However, existing microbiome studies largely rely on classical machine learning or shallow deep learning models that fail to capture higher-order microbial interactions, multimodal functional dependencies, and immune feasibility constraints simultaneously. Moreover, most approaches lack biological constraint enforcement, leading to predictions that may be statistically accurate but immunologically implausible. To address these limitations, this study introduces SIMT, the Synthetic Immune Modulation Transformer, a novel immune-aware deep learning framework for microbial interaction modelling and synthetic microbiota design. SIMT integrates a graph transformer for microbe-microbe interaction learning, a multimodal transformer for immune-associated functional inference, and a newly proposed Immune-Aware Constraint Layer (IACL) that enforces immune feasibility and homeostasis during optimization. The framework operates by learning weighted microbial interaction networks, integrating taxonomic abundance with inferred functional pathways, and constraining latent representations to physiologically meaningful immune ranges. The entire pipeline was implemented using Python-based deep learning libraries for scalable and reproducible analysis. Experimental evaluation demonstrated that the proposed approach achieved an F1-score of 96.41% and an AUC of 95.12%, outperforming existing microbiome-based models, including Random Forest, explainable RF frameworks, convolutional neural networks, fine-tuned language models, and regularized logistic regression reported in prior studies. Beyond predictive performance, SIMT enables immune-stable synthetic consortium optimization, offering interpretable and biologically grounded insights. Overall, the results confirm that immune-aware transformer modelling significantly advances microbiome analytics, supporting reliable in silico design of immune-compatible microbial communities for translational biomedical applications.