{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:17:10Z","timestamp":1787163430873,"version":"build-2736575974"},"reference-count":89,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2022,9,26]],"date-time":"2022-09-26T00:00:00Z","timestamp":1664150400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that they may also be implicated in IBD. In our study, we characterized these often-neglected eukaryotic microbial communities by identifying fungi and protozoa in published shotgun stool metagenomes from 355 people with IBD (206 with Crohn\u2019s disease, 126 with ulcerative colitis, and 23 with IBD-unclassified) and 471 unaffected healthy individuals. The individuals with IBD had a higher prevalence of fungi, particularly Saccharomyces cerevisiae, and a lower prevalence of protozoa, particularly Blastocystis species (subtypes 1, 2, 3, and 4). Regression analysis showed that disease state, age, and BMI were associated with the prevalence and abundance of these two genera. We also characterized the eukaryotic gut microbiome in a shotgun stool metagenomic dataset from people with IBD who received fecal transplants, with samples pre- and post-transplantation, and from their donors. We found that in some FMT recipients, a single eukaryotic species remained stable over time, while in other recipients, the eukaryotic composition varied. We conclude that the eukaryotic gut microbiome is altered and varies over time in IBD, and future studies should aim to include these microbes when characterizing the gut microbiome in IBD.<\/jats:p>","DOI":"10.3390\/microorganisms10101910","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T01:51:49Z","timestamp":1664329909000},"page":"1910","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5988-7887","authenticated-orcid":false,"given":"Gina L.","family":"Guzzo","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Murthy N.","family":"Mittinty","sequence":"additional","affiliation":[{"name":"School of Public Health, University of Adelaide, Adelaide, SA 5005, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5550-9176","authenticated-orcid":false,"given":"Bastien","family":"Llamas","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia"},{"name":"Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia"},{"name":"National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane M.","family":"Andrews","sequence":"additional","affiliation":[{"name":"Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Faculty of Health Sciences, Royal Adelaide Hospital & School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura S.","family":"Weyrich","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia"},{"name":"Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1056\/NEJM199109263251306","article-title":"Inflammatory bowel disease","volume":"325","author":"Podolsky","year":"1991","journal-title":"N. 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