Fig. 4: Impact of bacterial and fungal exometabolites on SynCom structure and metabolic profiles.

a Schematic of the MetaFlowTrain setup with sterile extract as input, 28 parallel trains, two microchambers per train, and two outputs: community profiles (MetaBarcoding) and exometabolites (targeted metabolomics. b Boxplots showing the abundances of microbial community members (log₁₀ reads) for different microchamber combinations. Boxplots are delimited by the first and third quartiles, with the central line representing the median value. Whiskers extend to show the range of the data within 1.5 * IQR from the quartiles, and all data points are displayed as individual points, including outliers. n = 7 independent microchamber trains * n = 11 bacteria (n = 77) or n = 4 fungi (n = 28) per treatment. Letters denote statistically significant differences between bacterial abundance or fungal abundance (Kruskal–Wallis test (P < 0.05), followed by two-sided Dunn’s post hoc tests with Benjamini-Hochberg correction for multiple comparisons (P < 0.05)). c Heatmap showing bacterial and fungal community composition across microchamber combinations. Red color intensity indicates log-transformed absolute abundances. Balloon plot shows the mean absolute abundance of microbial community members. n = 7 independent microchamber trains per treatment. Letters indicate statistically significant differences (Kruskal–Wallis test (P < 0.05), followed by two-sided Dunn’s post hoc tests with Benjamini-Hochberg correction for multiple comparisons (P < 0.05). d PCA plots displaying targeted metabolic profiles (n = 35 metabolites). n = 7 independent microchamber trains per treatment, except for B–F, n = 8 independent microchamber trains. Statistical significance was determined by PERMANOVA-based comparison of metabolic profiles (CanberraDistances~Time/SynComs, permutations = 999). The microchamber configuration is denoted as Microchamber1–Microchamber2 (e.g., B–F: Bacterial SynCom in microchamber 1 and Fungal SynCom in microchamber 2). Colors represent the different combinations of SynCom used in the microchambers. Source data are provided as a Source Data file.