This study was conducted in the animal house of the College of Education for Girls, to investigate the effect of beta-amino butyric acid (BABA) on the microorganisms in the digestive system of mice. The bacteria present in the stool were isolated and diagnosed. And that intestinal bacteria have an effective role in influencing human health. However, few factors that affect the bacteria in the digestive system are known. Despite the increase in the number of microbial communities colonizing the gastrointestinal tract, many of these bacteria have been found to possess virulence factors that can negatively affect the host organism and protect it from prevailing antibiotics. BABA) was used with four treatments (100, 200, 300, 0) mg/kg animal weight denoted by A, B, C, and D. Male rats were immersed orally in four doses per week, and the results showed that the amino acid effectively affected On the intestinal bacterial community, where the third concentration of the fourth dose gave the lowest rate of the number of bacterial isolates, which led to the elimination of a large number of them, followed by the second concentration and then the first compared to the comparison treatment that achieved the highest rate of the number of isolates. While histidine had no negative effect on the Toll-Like Receptor 4 (TLR4), the results showed that TLR4 was a normal receptor.