We collected detailed clinical metadata, fecal samples, and blood samples for 228 individuals in three cohorts: healthy controls, patients with short-term (<4y) or long-term (>10y) ME/CFS. A comprehensive ‘omics workflow was constructed with the multi-data types (phenotypic, metagenomics, and metabolomics, respectively) and multi-computational models to understand potential host-microbe interactions. LC-MS, Liquid chromatography-mass spectrometry.