Metatranscriptomics reveals the horse gut RNA virome and a viral sharing network with human and domestic animals

Introduction RNA viruses, a unique class of life forms, are widely distributed in nature and pose potential health risks. Monitoring the gut RNA virome in livestock is a crucial component of global health surveillance. As important companion animals, horses play a vital role in transportation and make significant contributions to various cultural and economic activities. Nevertheless, the characteristics of horse gut RNA viruses remain largely uncharted. Methods In this study, we used metatranscriptome sequencing and bioinformatics methods to characterize viruses within the gut contents of 16 horses spanning three breeds (Thoroughbred, Akhal-Teke and Yili horse). Results A total of 497 viral genomes from 22 viral families were recovered, including both double-stranded RNA (dsRNA) and single-stranded RNA (ssRNA) viruses, and encompassed positive- and negative-sense types commonly found in mammalian hosts. Among these, Picobirnaviridae was the most abundant RNA viral family in the horse gut. Beta diversity analyses revealed variations in RNA viral abundance across the three breeds, and differential analysis identified 82 RNA viruses exhibiting significant differences ( p < 0.05) between Akhal-Teke and Yili horses. Comparisons of coverage scores with other mammals revealed shared viral networks among intestinal RNA viruses of horses, humans, cows, and sheep. Discussion This study provides valuable data for future research on the horse gut RNA virome, shedding new light on the cryptic viral sharing network within the horse gut.