Fig. 1
From: An in vitro model maintaining taxon-specific functional activities of the gut microbiome
Establishment and general performance of the MiPro model. a Main components of the MiPro model: microbiome samples are cultured in an optimized culture medium in a 96-deep well plate. The plate is covered with a silicone-gel cover perforated at the top of each well. The plate is shaken at 500 rpm on a digital shaker. b Pearson’s correlation coefficient r of taxon-specific functional profiles between the inocula (0 h baseline sample) and 96-deep well-cultured microbiome with the presence of primary bile salts (CDCA + CA) or commercialized bile salts mixture (DCA + CA), as well as tube-cultured microbiome with the presence of primary bile salts. 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. n = 3 biologically independent microbiomes. c Increase in bacterial biomass over time in each individual microbiome (determination using absorbance at 595 nm). Colored ribbons indicate the range of standard deviations around the means (n = 4 technical replicates for each treatment). d Temporal microbiome viability changes as shown with flow cytometry. The gating strategy is shown in Supplementary Fig. 3. (e) Bacterial cell count in each flow cytometry recording. Data were recorded for 2 min on the low flow rate setting. Underlying data are provided in the Source Data file
