Highlights: • Reaction norms were used to assess the effect of nematode infection on fecal microbiota in three mouse strains. • Microbiota diversity declined along the gradient of infection with Heligmosomoides polygyrus. • The dissimilarity in the composition of the microbiota increased as H. polygyrus infective dose increased. • Dysbiosis might represent an indirect cost of helminth infection. Abstract: The gut microbiota constitutes a diverse community of organisms with pervasive effects on host homeostasis. The diversity and composition of the gut microbiota depend on both intrinsic (host genetics) and extrinsic (environmental) factors. Here, we investigated the reaction norms of fecal microbiota diversity and composition in three strains of mice infected with increasing doses of the gastrointestinal nematode Heligmosomoides polygyrus. We found that α-diversity (bacterial taxonomic unit richness) declined along the gradient of infective doses, and β-diversity (dissimilarity between the composition of the microbiota of uninfected and infected mice) increased as the infective dose increased. We did not find evidence for genotype by environment (host strain by infective dose) interactions, except when focusing on the relative abundance of the commonest bacterial families. A simulation approach also showed that significant genotype by environment interactions would have been hardly found even with much larger sample size. These results show that increasing parasite burden progressively depauperates microbiota diversity and contributes to rapidly change its composition, independently from the host genetic background.