Fig. 3: AA exposure promotes A. muciniphila in a simulated model of the human distal gut microbiota.

a Simplified schematic providing a detailed overview of experimental methodology. Servier Medical Art images were used and modified under the Creative Commons Attribution 3.0 Unported License. b Bar plot representing the microbiota compositions of gut model samples from before, during, and after AA exposure as determined by sequencing of the V4 region of the bacterial 16S rRNA gene. c PCA plot of time-course collected gut model samples matching the days shown. Aitchison distance of genus-level microbiota compositions were used as input values and strength of association for taxa are depicted by the length of arrows shown. d qPCR-based quantification of total bacteria, Enterobacteriaceae, and A. muciniphila in the gut model over time. e Relative amount of AA remaining in bacterial culture supernatants following 24 h incubation in 100 ppm. AA-supplemented media. Data shown represent the mean ± standard deviation (one-way ANOVA with Sidak’s multiple comparisons) for n = 3 biological replicates performed in technical triplicate for each bacterial strain. f Co-occurrence network visually illustrating the significant interactions between taxa in the gut model. g, h Representative growth curves and i carrying capacity (k) of bacteria in 0.25 mM AA and acetate-supplemented media. Data represent mean ± standard deviation (one-way ANOVA with Sidak’s multiple comparisons) of n = 3 biological replicates performed in technical triplicate for each bacterial strain. j, k Temporal overlay graphs showing A. muciniphila and Enterobacteriaceae abundances in the gut model over time alongside predicted menaquinone (vitamin K2) biosynthesis-related pathway abundances. RA = relative abundance. ****P < 0.0001 and n.s. = not significant.