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The black-necked crane (<jats:italic>Grus nigricollis<\/jats:italic>) is a near-threatened species and there is a shortage of research on its parasite diversity. Our study aimed to use noninvasive methods to detect intestinal parasites and pathogenic FLA in <jats:italic>G. nigricollis<\/jats:italic> using high-throughput sequencing (HTS) based on the 18S rDNA V9 region. A total of 38 fresh fecal samples were collected in Dashanbao, China, during the overwintering period (early-, middle I-, middle II-, and late-winter). Based on the 18S data, eight genera of parasites were identified, including three protozoan parasites: <jats:italic>Eimeria<\/jats:italic> sp. (92.1%) was the dominant parasite, followed by <jats:italic>Tetratrichomonas<\/jats:italic> sp. (36.8%) and <jats:italic>Theileria<\/jats:italic> sp. (2.6%). Five genera of helminths were found: <jats:italic>Echinostoma<\/jats:italic> sp. (100%), <jats:italic>Posthodiplostomum<\/jats:italic> sp. (50.0%), <jats:italic>Euryhelmis<\/jats:italic> sp. (26.3%), <jats:italic>Eucoleus<\/jats:italic> sp. (50.0%), and <jats:italic>Halomonhystera<\/jats:italic> sp. (2.6%). Additionally, eight genera of FLA were detected, including the known pathogens <jats:italic>Acanthamoeba<\/jats:italic> spp. (<jats:italic>n<\/jats:italic>\u00a0=\u00a013) and <jats:italic>Allovahlkampfia<\/jats:italic> spp. (<jats:italic>n<\/jats:italic>\u00a0=\u00a03). Specific PCRs were used to further identify the species of some parasites and FLA. Furthermore, the 18S data indicated significant changes in the relative abundance and genus diversity of the protozoan parasites and FLA among the four periods. These results underscore the importance of long-term monitoring of pathogens in black-necked cranes to protect this near-endangered species.<\/jats:p>","DOI":"10.1051\/parasite\/2024028","type":"journal-article","created":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T08:18:52Z","timestamp":1717143532000},"page":"28","source":"Crossref","is-referenced-by-count":3,"title":["Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living 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