Fig. 5

Net daily production (mmol day⁻¹) of acetate (A), propionate (B), butyrate (C) and total SCFA (D) was significantly affected by SHIME transit time variation (n = 30). (E) Net daily ammonium production (mmol day⁻¹) and SHIME transit time significantly correlated (n = 12, P = 1.08E-05, Spearman’s rank correlation). The biomass-normalised net acetate (F), propionate (G), butyrate (H) and total SCFA (I) production relative to the net biomass production (mmol total cells⁻¹) significantly changed with SHIME transit time (n = 30). The net carbohydrate-to-acetate (J), propionate (K), butyrate (L) and total SCFA (M) conversion efficiency, i.e. the net production relative to the daily carbohydrate utilisation (mmol g.⁻¹), was significantly affected by SHIME transit time (n = 30). Short, medium and long SHIME transit times were 8, 16 and 24h in the proximal colon and 13, 26 and 39h in the distal colon. Statistically significant differences between transit times are depicted by the letters a, b and c in panels A–D and F–M (unpaired two-sided Wilcoxon signed rank tests with Holm correction). Identical letters indicate no significant differences (P > 0.05). Significant differences between colon regions of the same transit time are marked with asterisks ( ∗) (P < 0.05, paired two-sided Wilcoxon signed rank tests with Holm correction). Box plots display individual data points, as well as the interquartile range, median and outliers beyond the 1.5 times interquartile range (whiskers)