Fig. 3

Differences in gene expression change among MHCO and Caco-2 after coculturing with B. longum. (A) A schematic representation of the experiment. (B) Colony-forming units (CFU) counts per milliliter of B. longum inoculated after 24-hour incubation with MHCO and Caco-2 using iHACS. (C) PCA of the transcriptomes of MHCO and Caco-2 cocultured with or without B. longum. Filled and unfilled circles indicate two independent experiments (each three replicates). Transcriptomes from three replicates were plotted. Ellipses indicate the 95% confidence interval. (D) Volcano plot depicting the upregulated and downregulated genes of Caco-2 (left panel) and MHCO (right panel) after coculturing with B. longum. The x- and the y-axis show the log₂ transformed fold change and the -log₁₀ transformed adjusted p-value. Red and blue dots indicate significantly upregulated and downregulated genes after coculturing with B. longum according to adjusted p-value < 0.05 and log₂ fold change > 2. (E) Venn diagram comparing the significantly upregulated (left panel) and downregulated genes (right panel) in MHCO or Caco-2 after coculturing with B. longum.