Fig. 3: Cytokine and transcriptional changes induced by bacterium F. prausnitzii in GuMI with APCs.

a Workflow of GuMI experiments including preparation of monolayer (green line), monocyte isolation and APC differentiation (orange line), hardware preparation (aqua), and bacterial culturing (blue line). Circles in the metro map indicate the critical tasks and the workload. Color blue in c and h–m is used to highlight the conditions with F. prausnitzii. b Schematic demonstration of co-culture of F. prausnitzii, colonic epithelium, and APCs. c TEER values of GuMI-APC with and without F. prausnitzii. Two-tailed unpaired t test. d–g Brightfield image (d), immunofluorescent staining of bacterial cells (e), epithelium (f), and APCs (g). Scale bar, 300 μm (d) and 30 μm (e–g). Staining, nucleic acids (blue, e–g) and green (beta-actin, f, g). h Live bacterial density of F. prausnitzii at 0 and 48 hours. ***: p < 0.001, two-tailed unpaired t test. i Volcano plot comparing cytokines/chemokines in apical media in the presence or absence of F. prausnitzii (GuMI-APC-FP vs. GuMI-APC-NB). j The significantly increased cytokine concentration in apical media shown in i. k Volcano plot on the comparison of cytokines or growth factors in basolateral media in the presence or absence of F. prausnitzii (GuMI-APC-FP vs. GuMI-APC-NB). l The concentration of significantly increased cytokine MCP1/CCL2 in basolateral media shown in k. i–l Multiple t test corrected by the Holm-Sidak method. m Transcriptional change of inflammation-related genes in colonic epithelial cells in GuMI-APC F. prausnitzii versus no bacteria. n = 3. Blue boxes indicate a <0.75-fold decrease or >1.5-fold increase, and black boxes indicate no significant difference. Two-tailed unpaired t test. Error bars in c, h, j, l represent standard deviation.