Two distinct classes of antibiotics (neomycin and vancomycin) seem to induce ER stress in colonic cells which decreases mucus production and increases risk of bacterial inflammation etc. The point is that there appears to be a direct effect on the host mouse physiology. There are other classes of antibiotics that do not have this effect, phage would likely be one of them (there is a theory that phage provided a persistent immunity by dwelling in the mucus).