18S rRNA gene metabarcoding for investigation of gastrointestinal parasite diversity in great cormorants

The great cormorant (Phalacrocorax carbo) is a migratory, fish-eating bird that may act as a carrier for various pathogens, raising potential ecological and public health concerns. This study investigated the diversity of gastrointestinal parasites in great cormorants from the Republic of Korea using 18S rRNA gene metabarcoding and conventional diagnostic methods. Fecal samples were collected from 10 great cormorants in Korea, and DNA was extracted for metabarcoding targeting the V4 and V9 regions of the 18S rRNA gene using the MiSeq platform. Conventional PCR and microscopic examination were used for validation. The V4 region of the 18S rRNA gene revealed the presence of Baruscapillaria spiculata, Contracaecum sp., and Isospora lugensae. The V9 region analysis identified the following parasites: Tetratrichomonas sp., Histomonas meleagridis, Trichomitus sp., Tetratrichomonas prowazekii, B. obsignata, Monosiga ovata, and Fasciola gigantica. Furthermore, conventional PCR confirmed the presence of Contracaecum sp., Isospora sp., and unspecified trichomonads, and microscopic examination identified eggs of capillarid, Contracaecum, and Eustrongylides and trophozoites of flagellated protozoa in the collected cormorant fecal samples. The findings underscored the potential ecological role of great cormorants as hosts for diverse gastrointestinal parasites and the utility of 18S rRNA gene metabarcoding for screening the diversity of gastrointestinal parasites in great cormorants.