Microbiome as a Diagnostic Tool: Identifying Resistance to Haemonchus contortus in Goats through Metagenomic Profiling

Abstract

Gastrointestinal nematodes (GINs), particularly Haemonchus contortus ( H. contortus ), pose significant challenges to small ruminant health and productivity, with increasing resistance to commercial anthelmintics. Conventional diagnostic techniques, such as fecal egg counts (FEC) and larval cultures (LC), are labor-intensive, time-consuming, and require technical expertise, limiting their practicality in field settings. There is an urgent need for faster, more accessible diagnostic tools to inform treatment decisions and improve parasite management strategies. In this study, we hypothesized that changes in microbiota, specifically shifts in microbial richness, community composition, and consistency, can serve as reliable biomarkers for infection and resistance. To test this hypothesis, we employed a metagenomic approach to characterize microbial communities in Alpine wethers based on their GIN infection status. Animals were divided into four groups: uninfected controls, infected-only, infected and treated with zoledronic acid (a bisphosphonate, previously believed to act as an antibiotic), and infected and treated with a neutralizing antibody targeting γδ T cells. Metagenomic analyses of tissue samples revealed distinct microbial signatures associated with host susceptibility or resistance. Infection with H. contortus was linked to inflammatory microbial profiles, which varied depending on the treatment and infection status. Our findings suggest that inflammation-associated microbial taxa could serve as indicators of parasitic infection, supporting the development of more precise, data-driven diagnostic tools for early detection of haemonchosis. Additionally, by identifying microbiota-based markers of resistance, this research paves the way for more sustainable parasite control strategies, including microbiota manipulation and fecal microbiota transplantation. Overall, metagenomics provides a robust framework for investigating host-pathogen interactions and uncovering novel approaches to combat parasitism in livestock.