MetPA network tools were utilized to further analyze the effects of different concentrations of MSNs on the metabolic pathways of E. coli. As shown in Fig 9, we found that glycine, serine and threonine metabolism, as well as beta-alanine metabolism, but also the metabolisms of carboxylic acids such as pyruvate and butanoate were all significantly affected by exposure to 1000 μg/mL of MSNs. The pathway analysis results were almost the same as in the ones shown in Fig 9, wherein E. coli was exposed to 1 μg/mL, 10 μg/mL, or 100 μg/mL (S1, S2 and S3 Figs). These results confirmed that MSNs could indeed significantly affect the amino acid-related metabolic pathways. As discussed above, due to stress response mechanisms found in many microorganisms, E. coli might modulate amino acid- or protein-related metabolic pathways to adapt to the adverse environment.