The purpose of this research is to estimate and quantify the toxicity of titanium dioxide ($TiO_2$) nanoparticles in microorganisms. Nano-sized particles of $TiO_2$ were more toxic compared to micro-sized particles. Three microorganismal species, Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, were used to test $TiO_2$ antimicrobial effects. E. coli showed the lowest survival rate (36%), while S. cerevisiae showed the highest survival rate (71%). The antimicrobial effect of $TiO_2$ was also dependent on ultraviolet ray wavelength. The survival ratio of E. coli was 40% at a 254 nm wavelength and 80% at 365 nm. To observe the effect of $TiO_2$ on the intracellular metabolism, a metabolic flux analysis and the measurement of in vivo glucose-6-phosphate were performed. G6P concentration in cells exposed to $TiO_2$ increased, and glycolysis flux was also higher than the controls.