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In a set of faecal samples collected from asymptomatic children of six distant populations, we first assessed the community profiles of protist 18S rDNA and then characterized<jats:italic>Blastocystis<\/jats:italic>subtypes and tested<jats:italic>Blastocystis<\/jats:italic>association with the faecal bacteriome community.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Stool samples were collected from 244 children and young persons (mean age 11.3\u00a0years, interquartile range 8.1\u201313.7) of six countries (Azerbaijan 51 subjects, Czechia 52, Jordan 40, Nigeria 27, Sudan 59 and Tanzania 15). The subjects showed no symptoms of infection. Amplicon profiling of the 18S rDNA was used for verification that<jats:italic>Blastocystis<\/jats:italic>was the most frequent protist, whereas specific real-time PCR showed its prevalence and quantity, and massive parallel amplicon sequencing defined the<jats:italic>Blastocystis<\/jats:italic>subtypes. The relation between<jats:italic>Blastocystis<\/jats:italic>and the stool bacteriome community was characterized using 16S rDNA profiling.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p><jats:italic>Blastocystis<\/jats:italic>was detected by specific PCR in 36% (88\/244) stool samples and was the most often observed faecal protist. Children from Czechia and Jordan had significantly lower prevalence than children from the remaining countries. The most frequent subtype was ST3 (49%, 40\/81 sequenced samples), followed by ST1 (36%) and ST2 (25%). Co-infection with two different subtypes was noted in 12% samples. The faecal bacteriome had higher richness in<jats:italic>Blastocystis<\/jats:italic>-positive samples, and<jats:italic>Blastocystis<\/jats:italic>was associated with significantly different community composition regardless of the country (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.001 in constrained redundancy analysis). Several taxa differed with<jats:italic>Blastocystis<\/jats:italic>positivity or quantity: two genera of Ruminococcaceae were more abundant, while<jats:italic>Bifidobacterium, Veillonella, Lactobacillus<\/jats:italic>and several other genera were undrerrepresented.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Asymptomatic children frequently carry<jats:italic>Blastocystis<\/jats:italic>, and co-infection with multiple distinct subtypes is not exceptional. Prevalence and quantity of the organism clearly differ among populations.<jats:italic>Blastocystis<\/jats:italic>is linked to both faecal bacteriome diversity and its composition.<\/jats:p><\/jats:sec><jats:sec><jats:title>Graphical Abstract<\/jats:title><\/jats:sec>","DOI":"10.1186\/s13071-021-04859-3","type":"journal-article","created":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T09:03:03Z","timestamp":1628758983000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome"],"prefix":"10.1186","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0526-8714","authenticated-orcid":false,"given":"Ondrej","family":"Cinek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katerina","family":"Polackova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasha","family":"Odeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abeer","family":"Alassaf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lenka","family":"Kramn\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"MaryAnn Ugochi","family":"Ibekwe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edna Siima","family":"Majaliwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunduz","family":"Ahmadov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bashir Mukhtar Elwasila","family":"Elmahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanan","family":"Mekki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sami","family":"Oikarinen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Lebl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed Ahmed","family":"Abdullah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"key":"4859_CR1","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s40168-020-00875-0","volume":"8","author":"G Berg","year":"2020","unstructured":"Berg G, Rybakova D, Fischer D, Cernava T, Verges MC, Charles T, et al. 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