Probiotics affect intestinal metabolism and play a crucial role in gut homeostasis. Studies on probiotic effector molecules—bacteriocins, peptidoglycan, teichoic acid, exopolysaccharides, secretory proteins, and short-chain fatty acids—describe their effect on the gut barrier; immune and nervous system; and gut microbiota. However, the detailed mechanism of how the intestinal microbiota changes after the intervention of effector molecules remains unknown. More recently, owing to a rare systematic review about the function of effector molecules in the intestinal tract, it has become vital to discover the molecular model of action of how the gut environment is affected by probiotics. Here, we review the characteristics of effector molecules from probiotics and the advances in understanding the interactive patterns between effector molecules and the gut microenvironment. CLICK TO REVIEW