A Novel Index for Predicting Health Status Using Species-level Gut Microbiome Profiling

Development of a biologically-interpretable and robust metric for evaluating health status based on gut microbiome remains an important target in human microbiome research. We introduce the Gut Microbiome Health Index (GMHI), a computational tool that determines the degree to which a gut microbiome profile reflects wellness or illness. GMHI was formulated based on microbial species specific to healthy gut ecosystems. These were identified through a multi-study, integrative analysis on 4347 human stool shotgun metagenomes from 34 published studies across healthy and 12 non-healthy conditions. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of health compared to alpha-diversity indices generally considered as markers for gut health or dysbiosis. Validation of GMHI on 679 samples from 9 additional studies resulted in remarkable reproducibility in distinguishing healthy and non-healthy groups. Our findings suggest that gut taxonomic signatures may serve as universal predictors of health and disease.