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While many studies apply targeted amplicon sequencing, here we used untargeted metagenomics to simultaneously identify protists and helminths in pre-diagnosed faecal and tissue samples. The approach starts from RNA and operates without an amplification step, therefore allowing the detection of all eukaryotes, including pathogens, since it circumvents the bias typically observed in amplicon-based HTS approaches. The generated metagenomics datasets were analysed using the RIEMS tool for initial taxonomic read assignment. Mapping analyses against ribosomal reference sequences were subsequently applied to extract 18S rRNA sequences abundantly present in the sequence datasets. The original diagnosis, which was based on microscopy and\/or PCR, could be confirmed in nearly all cases using ribosomal RNA metagenomics. In addition to the pre-diagnosed taxa, we detected other intestinal eukaryotic parasites of uncertain pathogenicity (of the genera <jats:italic>Dientamoeba, Entamoeba, Endolimax, Hymenolepis<\/jats:italic>) that are often excluded from routine diagnostic protocols. The study clearly demonstrates the applicability of untargeted RNA metagenomics for the parallel detection of parasites.<\/jats:p>","DOI":"10.1007\/s00436-020-06754-9","type":"journal-article","created":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T07:02:31Z","timestamp":1593154951000},"page":"2623-2629","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Untargeted metagenomics shows a reliable performance for synchronous detection of parasites"],"prefix":"10.1007","volume":"119","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0436-4480","authenticated-orcid":false,"given":"Claudia","family":"Wylezich","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone M.","family":"Caccio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Walochnik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Beer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dirk","family":"H\u00f6per","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,26]]},"reference":[{"key":"6754_CR1","doi-asserted-by":"publisher","first-page":"4413","DOI":"10.1128\/JCM.40.12.4413-4417.2002","volume":"40","author":"J Blessmann","year":"2002","unstructured":"Blessmann J, Buss H, Nu PA, Dinh BT, Ngo QT, Van AL, Alla MD, Jackson TF, Ravdin JI, Tannich E (2002) Real-time PCR for detection and differentiation of Entamoeba histolytica and Entamoeba dispar in fecal samples. 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Samples were fully anonymised, the sole information linked to the samples was being positive or negative for the respective parasite in the respective diagnostic test.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}