The association between fecal microbiota, age and endoparasitism in adult alpacas

Endoparasitism is a major cause of morbidity and mortality in alpacas, with growing emergence of anthelmintic resistance. The purpose of the study was to correlate nematode worm burden and selected host phenotypic characteristics, such as age and weight, with the composition of the intestinal microbiota of adult alpacas. Fecal samples were collected per rectum from healthy adult alpacas at 3 separate timepoints at a single farm. The profile of the fecal bacterial microbiota was characterized using 16S amplicon sequencing. Serial clinical exams and fecal egg counts were compared using related samples analyses. The fecal microbiota of identically managed, healthy alpacas was characterized by a high level of temporal stability, as both alpha and beta-diversity significantly correlated between sampling timepoints. Pairwise beta diversity between samples collected at each timepoint was low, ranging from 0.16 to 0.21 UniFrac distance units. The intensity of strongylid nematode infection, including Haemonchus, Ostertagia, Trichostrongylus, was only significantly correlated with microbiota composition in samples collected 14 days after treatment with levamisole. Analysis of similarity revealed no clustering of microbiota from anthelmintic responders or non-responders. Alpaca age explained the largest proportion of fecal microbiota variation and was the only consistently significant predictor of fecal microbiota taxonomic composition, by impacting the ratio of relative Bacteroidetes and Firmicutes abundance. Firmicutes, mostly Clostridiales, was the most abundant taxon across all collections.