Despite recent progress in the diagnosis and treatment of advanced cancers, the overall patient treatment outcome did not substantially improve over the last years. Therefore, developing novel therapies, which may also work synergistically in combination with the conventional therapies is crucial. One promising new therapeutic approach is bacterium-mediated cancer therapy. In the current work, we describe the influence of the gut microbiome and intranasal E. coli Nissle applications on the metabolism in cancer tissues of 4T1 syngeneic tumor bearing mice. Here we found that after gut microbiome depletion and/or E. coli Nissle treatment the ratios of ADMA/Arginine, Putrescine/Ornithine and Kynurenine/Tryptophan as well as the total concentration of Carnosine, Kynurenine and H1 (synonymus for all sugars detectable) are significantly altered in tumor tissues of as the result of treatment. In conclusion, our current data show that E. coli Nissle bacteria facilitating metabolic modulation of tumors, a finding could be important for improved cancer therapy in patients.