The aim of this study was to assess the impact of abiotic (physicochemical factors) and biotic (intestinal microbiota, probiotics) parameters from the human gut on the survival and virulence of EHEC O157:H7 by using complementary in vitro (human artificial digestive systems) and in vivo (mice ileal loops, human-microbiota associated rats) approaches. We have shown that differences in physicochemical parameters of the human upper gastrointestinal tract may partly explain why children are more susceptible to EHEC infections than adults. In addition, the human gut microbiota was shown to modulate EHEC O157:H7 virulence suggesting that it could influence the clinical outcome of the infections. Lastly, our data indicate that the probiotic yeast strain Saccharomyces cerevisiae CNCM I-3856 may be useful in the fight against EHEC pathogens by limiting the amount of bacteria reaching the colon, beneficially modulating gut microbiota activity, decreasing toxin-encoding genes expression, and inhibiting EHEC tropism to intestinal Peyer’s patches. Such data provide a more complete picture of EHEC pathogenesis in the human gut and a better understanding of the mechanisms related to the antagonistic effects of probiotics.