Fig. 2

Metaproteomics revealed taxonomic & functional composition stability over time. a Principal coordinate analysis (PCoA) plot with Bray-Curtis dissimilarity on species level. b Compositional bar chart showing species-level biomass distribution over time in the cultured microbiome of V1 (see Supplementary Fig. 5 for V2 and V3). c PCA scores plot with hierarchical clustering based on COG functional categories of individual V1 (see Supplementary Fig. 9 for individuals V2 and V3). d Pearson’s correlation coefficient r of taxon-specific functional profiles between microbiome cultured over time and the baseline inoculum sample of V1 (see Supplementary Fig. 10 for V2 and V3; different letters indicate significant differences at the p = 0.05 level, Tukey-b test; box spans interquartile range (25th to 75th percentile), and line within box denotes median. Whiskers represent min to max values). For 0 h, Mipro 9 h, BCM 24 h and 34 h, n = 4 technical replicates; for Mipro 24 h, 34 h and 48 h, BCM 9 h, and 48 h, n = 4 technical replicates. e Visualization of associated taxa-functions enrichment analysis between 24 h MiPro-cultured and 0 h baseline samples in V1 (top 30 correlations were shown). Width of blocks and linkages represents number of matched proteins. Gray letters indicate un-paired pathways within the top 30 connections. f Pearson’s correlation coefficient r of taxon-specific functional profiles between the baseline inoculum and microbiome cultured in MiPro over a 5-day period. n = 3 technical replicates. g Compositional bar chart showing species-level biomass distribution of a gut microbiome cultured in MiPro over a 5-day period. Underlying data are provided in the Source Data file