Fig. 1
A Cell concentrations (cells mL−1) and SHIME transit time (proximal colon (PC) = 8, 16 and 24h; distal colon (DC) = 13, 26 and 39h) significantly correlated (n = 60, P = 4E-99, Spearman’s rank correlation). B Total cell concentrations (cells mL−1) significantly increased with SHIME transit time (n = 60). C The faecal cell concentrations (cells g−1) from the six donors increased with their self-assessed corn in vivo transit time (n = 12, Table S1). D–E The carbohydrate-to-total cell conversion (cells g−1) significantly decreased with SHIME transit time (n = 15 per donor, P = 1.35E-12). F The percentage of intact microbial cells (%) decreased with SHIME transit time (n = 60). Statistically significant differences between SHIME transit times are indicated by the letters a, b and c in panels B, E and F (unpaired two-sided Wilcoxon signed rank tests with Holm correction). Identical letters indicate no significant differences (P > 0.05). Significant differences between colon regions are indicated with asterisks (*) (P < 0.05, paired two-sided Wilcoxon signed rank tests with Holm correction). Box plots display the interquartile range, median and outliers beyond the 1.5 times interquartile range (whiskers). In A and F, individual data points are added