Fig. 1

Rapid Assay of Individual Microbiome (RapidAIM) workflow and performance. a Experimental, analytical, and bioinformatics components of the RapidAIM workflow. Each individual’s gut microbiome samples are cultured with the test compounds in a 96-well deep-well plate at 37 °C in strict anaerobic conditions for 24 h followed by high-throughput sample preparation and rapid LC-MS/MS analysis. Peptide and protein identification and quantification, taxonomic profiling, and functional annotation were performed using the automated MetaLab software [27]. b A series of six dilutions (dilution gradients: GRD1~6) of a same microbiome sample was tested in triplicates through the equal-volume digestion and equal-volume MS loading protocol; the summed peptide intensity was compared with a set of protein concentration standards provided with DC protein concentration assay and showed good linearity (center points and error bars represent mean ± SD). c Stacked bars of clusters of orthologous groups (COG) category levels across the six concentrations showing no bias at the functional quantifications. d PCA based on LFQ intensities of protein groups for all POC samples