The effect of a partial anthelmintic clearance on microbial communities along the gastrointestinal tract in goats challenged with Haemonchus contortus

In this study, we examined the ability of a partial anthelmintic clearance in restoring the altered microbial composition and function in the gut of Haemonchus contortus-infected goats. Our results showed a single-dose treatment with the anthelmintic drug Cydectin restored abomasal pH to the baseline level and resulted in an 83.9% and 61.8% reduction in fecal egg counts (EPG) and worm burden, respectively (P < 0.01). The treatment significantly reduced microbial richness indices, but only in the proximal colon. The anthelmintic increased the abundance of Proteobacteria, particularly that of Campylobacter in the colon. The anthelmintic treatment significantly affected several basic pathways in the midgut and hindgut, including bacterial secretion, butyrate metabolism, and LPS biosynthesis. Several network modules displayed a strong correlation with EPG and worm burden. The Mantel test unraveled a strong correlation between treatment related network topologies of the OTUs belonging to Actinobacteria and Rikenellaceae and EPG and worm burden significance, respectively. The treatment seemingly reduced the cellulolytic capacity in the colon. Furthermore, microbial signatures that can better predict anthelmintic outcomes were identified using a balance-based algorithm. Our findings provided novel insights into intimate interactions between the microbiome and Haemonchus parasite within the caprine gut and potential negative consequence of a partial anthelmintic clearance on animal health and well-being.