The effects of teeth-blackening bacteria Enterobacter ludwigii on the physiological system were investigated using the model organism Drosophila melanogaster. The bacteria were mixed with the fly food, and its effect was checked on the growth, development and behaviour of Drosophila. Microbes generate reactive oxygen species (ROS) within the haemolymph of the larvae once it enters into the body. The increased amount of ROS was evidenced by the NBT assay and using 2',7'-dichlorofluorescin diacetate dye, which indicates the mitochondrial ROS. The increased amount of ROS resulted in a number of abnormal nuclei within the gut. Besides that larvae walking became sluggish in comparison with wild type although the larvae crawling path did not change much. Flies hatched from the infectious larvae have the posterior scutellar bristle absent from the thorax and abnormal mechanosensory hairs in the eye, and they undergo time-dependent neurodegeneration as evidenced by the geotrophic and phototrophic assays. To decipher the mechanism of neurodegeneration, flies were checked for the presence of four important bioamines: tyramine, cadaverine, putrescine and histamine. Out of these four, histamine was found to be absent in infected flies. Histamine is a key molecule required for the functioning of the photoreceptor as well as mechanoreceptors. The mechanism via which mouth infectious bacteria E. ludwigii can affect the development and cause age-dependent neurodegeneration is explained in this paper.