The host microbiome is an integral component of animal physiology, contributing broadly to host health. However, little is known about the relationship between gut microbiota and response to enteric pathogens. Gastrointestinal helminth infections in production animals are a major impediment to agricultural output, thus we investigated the link between the gut microbiota of sheep and parasite infection. We used a cohort of 28 merino sheep assumed, based on selective breeding, to have differing levels of resistance to gastrointestinal nematode infection. Each sheep was infected with 14,000 Haemonchus contortus larvae. Faecal egg counts revealed a range of parasite burdens in the 28 sheep, with a significant difference in egg counts among the highest burden (n=5) and lowest burden (n=5) sheep. Bacterial community analysis of sheep faeces was conducted over an 8-week period (4 weeks pre- and 4 weeks post-infection) using automated ribosomal intergenic spacer analysis and partial 16S rDNA gene sequencing. Focusing on sheep with the highest burden (n=5) and lowest burden (n=5) of H. contortus infection, we found a markedly different microbial community structure in the two groups. Phylum level analysis revealed that Firmicutes were significantly more abundant in low-burden sheep, whereas Bacteriodetes and Proteobacteria were significantly more abundant in high-burden sheep. We also observed a greater change in the microbial composition in sheep with a high burden of parasites relative to low-parasite-burden sheep 3-4 weeks after the parasite infection was established. Interestingly, the three aforementioned phyla (Firmicutes, Bacteriodetes and Proteobacteria) all underwent significant changes in abundance; becoming more like the gut microbiota of pre-infection, low-burden sheep . Our data suggest a potential relationship between the microbiota and resistance to gastrointestinal parasite infection; and in recovery from infection; which could have important implications for animal production. The implications for human health are currently unknown, but warrant further investigation.