We propose an in vitro intestinal tube-shaped device with a secreted mucin layer that enables us to achieve stable and continuous co-culturing with bacteria. Our tube-shaped device is made of collagen hydrogel and has 3D crypt-like structures created by electrolytically generated microbubbles. Bacterial suspension can be perfused via glass/silicone tubes attached at both ends of the tube device. Supply of culture medium diffused from the outside of the tube ensures a stable culture of Caco-2 and HT29 cells on the inside of the tube. We confirmed that HT29 cells mainly secreted a mucin layer in the apical portion of cryptic structures that spatially separates the intestinal cells and bacteria as seen in vivo environments. As a result, the co-culture of intestinal cells and lactobacillus in vitro was demonstrated in the 3D crypt-like structures in our intestinal tube-shaped device.