{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T16:08:14Z","timestamp":1790784494579,"version":"4.1.0"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    The gut eukaryome, comprising the protists and fungi that fall within the strict definition of the microbiota together with the macroscopic helminths and arthropods that lie outside it, is under-detected by clinical microscopy and by short-read 16S\/18S sequencing, yet is increasingly implicated in inflammatory and autoimmune disorders, including psoriasis. Existing 18S V4\/V9 primers either lack cross-kingdom universality or fail to discriminate closely related species. We designed and evaluated broad-range PCR primers anchored in conserved blocks of nuclear 18S and 28S ribosomal genes, flanking a 1.0\u20133.5 kb cassette spanning the 3\u2032-end of 18S, ITS1, 5.8S, ITS2, and the 5\u2032-end of 28S. Stool samples from 91 plaque-psoriasis patients and 92 matched controls were collected; a subset of 32 samples was profiled by Oxford Nanopore amplicon sequencing using the EPI2ME wf-metagenomics pipeline (Kraken + Bracken) against the NCBI core_nt database. The gut eukaryome was dominated by Ascomycota and Protista, with 51 species-level entries assigned to\n                    <jats:italic>Candida<\/jats:italic>\n                    (37 named binomials), 27 entries assigned to\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    (12 subtype-labelled entries), 20 entries assigned to Malassezia (15 named species), and 37 entries assigned to\n                    <jats:italic>Cladosporium<\/jats:italic>\n                    recovered from a single PCR tube.\n                    <jats:italic>Blastocystis hominis<\/jats:italic>\n                    was detected in 37.5% of subjects (\u226550-read threshold; mean 7.5% in carriers), with concurrent detection of 12 subtype-labelled entries (ST1-ST4, ST7, ST10-ST15, ST24) and 11 named isolate entries. Psoriasis-relevant\n                    <jats:italic>Candida<\/jats:italic>\n                    species, such as\n                    <jats:italic>C. albicans<\/jats:italic>\n                    (34.4%),\n                    <jats:italic>C. tropicalis<\/jats:italic>\n                    (34.4%),\n                    <jats:italic>C. parapsilosis<\/jats:italic>\n                    (31.2%), and\n                    <jats:italic>Malassezia restricta<\/jats:italic>\n                    (9.4%; up to 12.1%) were co-detected. Long-read sequencing of a broad-range 18S -28S rRNA gene cassette provides a single-tube workflow for the simultaneous recovery of fungal, protistan, and plant-derived eukaryotic sequences from human stool.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1904425","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T15:32:35Z","timestamp":1790782355000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Targeted long-read eukaryotic profiling of human stool by broad-range 18S\u201328S rRNA gene amplicon sequencing on Oxford Nanopore Technologies: a proof-of-concept study"],"prefix":"10.3389","volume":"17","author":[{"given":"Ruslan","family":"Kalendar","sequence":"first","affiliation":[{"name":"Helsinki Institute of Life Science (HiLIFE), University of Helsinki","place":["Helsinki, Finland"]},{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asset","family":"Daniyarov","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]},{"name":"Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulykbek","family":"Kairov","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samat","family":"Kozhakhmetov","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dauren","family":"Yerezhepov","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bakytgul","family":"Yermekbayeva","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dos","family":"Sarbassov","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Almagul","family":"Kushugulova","sequence":"additional","affiliation":[{"name":"Center for Life Sciences, National Laboratory Astana, Nazarbayev University","place":["Astana, Kazakhstan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1111\/jeu.12691","article-title":"Revisions to the classification, nomenclature, and diversity of eukaryotes","volume":"66","author":"Adl","year":"2019","journal-title":"J. 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