In sickness and in health: profiling the bovine fecal eukaryome using optimized 18S metabarcoding with a mammal-blocking primer

Introduction

Calf diarrhea, caused by the apicomplexan pathogen Cryptosporidium parvum (C. parvum), poses significant economic and production challenges to the livestock industry. While 16S rRNA sequencing has advanced understanding of the bovine bacterial gut microbiota, the eukaryotic community remains underexplored due to methodological constraints, notably host DNA contamination. This study aimed to optimize an 18S rRNA metabarcoding workflow using mammal-blocking primers for bovine fecal eukaryome profiling and to characterize eukaryotic community differences between healthy and naturally C. parvum-infected diarrheic calves.