Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host

•Many small RNAs in extracellular vesicles (EVs) from diverse nematodes derive from intergenic and repetitive elements.•The parasite microRNA (miRNA) content of EVs is consistent across multiple EV isolation protocols and laboratories.•Trichuris muris and Heligmosomoides bakeri EVs contain distinct parasite miRNA family members.•Trichuris muris EVs purified across different laboratories consistently contain more mouse miRNAs than H. bakeri.•Comparisons of helminth EV cargos could help identify sRNAs involved in cross-species communication and niche specificity.