The effect of moxidectin on the faecal microbiome of horses with low parasite burdens

Anthelmintic treatment in horses is a risk factor for intestinal disease, currently the effect of anthelmintic on the hindgut microbiome is unknown. Objectives: To characterise (1) faecal microbiota, (2) feed fermentation kinetics (3) the metabolome following moxidectin administration to horses with very low (0 epg) parasite burdens. Hypothesis: Moxidectin will not alter (1) faecal microbiota, (2) feed fermentation, or, (3) host metabolome. Seventeen horses were randomly assigned to moxidectin treatment (n = 9) and control (n = 8) groups. Faecal and urine samples were collected before (0 hours) then 16, 40 and 160 hours after treatment. Response to medication was assessed by 16S rRNA sequencing of faecal microbiota, in vitro feed fermentation (moxidectin n = 4 control n = 3), and proton nuclear magnetic resonance (1H NMR) spectroscopy. Differences in taxa abundance between treatment groups were identified using LEfSe and the metabolome predicted using PICRUSt. Metabolite profiles were analysed by multi-variate discriminant analysis. Fermentation data were analysed by generalised linear mixed effects models. Moxidectin had a small but measurable effect on microbiota composition, with increased abundance of Deferribacter spp. and Spirocheates observed after 160 hours. Reduced in vitro fermentation was observed at 16 and 40 hours following moxidectin administration (p = 0.001). Lower pH of in vitro fermentations was observed 16 hours after moxidectin treatment. Metabolite profiles from in vitro fermentations differed between groups 16 hours after moxidectin (R2 = 0.69, Q2Y = 0.48), and within the moxidectin group between 16 hours and 160 hours post moxidectin (R2 = 0.79, Q2Y = 0.77). Findings suggest that in horses with low parasite burdens moxidectin had a small but measurable effect on the microbiome. These data are consistent with the hypothesis that parasite death is responsible for perturbation of the microbiome rather than anthelmintics per se.