Human microbiota are ecological communities of microbes colonized on and inside human bodies. The diverse microbes shape our body functions and are associated with a vast majority of human diseases. Many efforts have been made to deploy human microbiota for disease diagnostics and therapeutics, yet few of them turned out successful. One big issue arises from the highly interconnected nature of microbiota. To date, no approaches have disentangled the complicated relationship among microbes. Also, the diversity of microbes makes cross-cohort problem a challenge. We plan to solve these issues by developing a comprehensive and robust deep learning-based approach, which aims to bring microbiome-based diagnostics and therapeutics to reality.