Topology-Enabled Integration of Taxonomic and Functional Microbiome Profiles Reveals Distinct Subgroups in Healthy Individuals

Slides from a talk presented at ISMB/ECCB 2025 (Liverpool, UK) in the CAMDA (Critical Assessment of Massive Data Analysis) track. A pilot study was conducted to address two questions: (1) how to integrate diverse gut microbiome data modalities, and (2) what the shape of a “healthy” gut microbiome looks like. Topological data analysis was used to integrate taxonomic profiles, functional profiles, and health-related metadata from over 1,600 samples from healthy individuals. The results challenge the assumption of a single, uniform healthy state. Even within the healthy cohort, distinct subgroups emerged. These findings highlight the need for a more nuanced, data-driven microbiome health index that accounts for underlying complexity.