Metatranscriptomic surveillance reveals overlooked liver-associated parasite diversity and broad host ranges in small mammals from southern China

Parasite communities in the internal organs of small mammals remain poorly characterized because metatranscriptomic pathogen discovery has largely focused on viruses and bacteria. We individually sequenced liver transcriptomes from 351 small mammals collected across 14 cities in Guangdong Province, China, and combined sequence-based detection with phylogenetic, abundance, transcriptional, and morphological analyses. Parasites were detected in 148 animals (42.2%). Four liver-associated taxa were identified, including three putatively novel or highly divergent lineages. Trichinellidae sp1 dominated the community, occurring in 36.2% of animals (127/351), five host species spanning Rodentia and Eulipotyphla, and all surveyed cities. Hydatigera taeniaeformis occurred in 3.7% (13/351), and its identification was supported by hepatic cysts and morphologically recovered strobilocerci. Eucoccidiorida sp1 and Trypanosoma sp1 were detected sporadically. Mapping to available reference genomes revealed transcripts from multiple genes and functional categories, supporting genuine biological signals rather than isolated marker-gene matches. Amsterdam virus covaried with Trichinellidae sp1 (r = 0.59), whereas Wenzhou tapeworm virus 1 covaried with H. taeniaeformis (r = 0.47). These findings reveal an unexpectedly prevalent, phylogenetically diverse, and broadly distributed liver-associated parasite community and establish individual-organ metatranscriptomics as a useful framework for parasite discovery and surveillance.