Intestinal parasitic worms (commonly named intestinal helminths) affect close to one quarter of the world population and cause major losses for the livestock industry. These parasites establish chronic infections by modulation the immunity of their host. The immune system of mammals has been challenged by this immuno-modulation all along the course of evolution. Although intestinal parasites constitute a threat to human health, their recent eradication from industrialized regions may not be without consequence. In fact, the loss of intestinal helminth-driven immuno-regulation has been proposed to underlie the increased frequency of immune disorders observed in developed areas. Here, we first showed that one immune-modulatory strategy of intestinal helminths involves alterations of the intestinal bacterial communities. Although a lot remained to be understood about these alterations, they were characterized by higher intestinal levels of short-chain fatty acids (SCFAs), bacterial metabolites with immuno-suppressive activity. A better understanding of how intestinal helminths modulate host immunity via the intestinal microbiome may open the door to novel strategies to fight both intestinal parasites and immune disorders. In this context, I further characterized the impact of intestinal helminths on fecal bacterial communities in children living in a rural region of Ecuador and naturally infected with Ascaris lumbricoides, a parasite affecting 1.2 billion people worldwide. I then used a mouse model to extensively characterize the impact of intestinal helminth infection on intestinal bacterial communities along the intestinal tract. Based on our main results, we hypothesized that the worm-induced mucus secretion may favor the growth of SCFA-producing bacteria in the intestine, which in turn down-regulates the host immunity by promoting regulatory T cells. As part of this work, I also developed a web-based platform to assist scientists in analyzing data from high-throughput nucleic-acid sequencing, a method commonly used to characterize microbial communities but for which data analysis remains particularly challenging.