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While bacterial dysbiosis is well documented in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), fungal contributions and bacterial-fungal interactions remain underexplored, particularly in non-Western populations. We profiled bacterial (16S rRNA) and fungal (ITS) communities from stool samples of Saudi participants with IBS, ulcerative colitis (UC), Crohn\u2019s disease (CD), and controls. Analyses incorporated bacterial enterotypes, succinotypes, and\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    carriage to explore ecological and metabolic stratification. Differences in community composition were largely explained by GI disorder, host factors, enterotype, and\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    carriage, accounting for 1\u20139% of bacterial and fungal variation. IBS patients exhibited increased bacterial richness and evenness, whereas UC and CD displayed stronger fungal dysbiosis. Enterotyping identified two\n                    <jats:italic>Bacteroides<\/jats:italic>\n                    -dominant clusters: Bact1 (with\n                    <jats:italic>Faecalibacterium<\/jats:italic>\n                    ,\n                    <jats:italic>Alistipes<\/jats:italic>\n                    ) and Bact2 (enriched in\n                    <jats:italic>Escherichia-Shigella<\/jats:italic>\n                    ,\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    ), with Bact2 linked to reduced diversity and elevated calprotectin. Succinotyping distinguished\n                    <jats:italic>Dialister<\/jats:italic>\n                    -dominant (D-type) and\n                    <jats:italic>Phascolarctobacterium<\/jats:italic>\n                    -dominant (P-type) communities; UC was enriched in fragile, bridge-dependent D-type networks, in contrast to resilient, short-chain fatty acid (SCFA)- and H\n                    <jats:sub>2<\/jats:sub>\n                    S-producing P-type networks.\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    was detected in 48% of participants (mainly subtypes 1 (ST1) and ST3). It was associated with enrichment of butyrate-producing bacteria (\n                    <jats:italic>Roseburia<\/jats:italic>\n                    ,\n                    <jats:italic>Anaerobutyricum<\/jats:italic>\n                    ,\n                    <jats:italic>Butyribacter<\/jats:italic>\n                    ) and distinct fungal genera, with subtype-specific signatures (ST1 enriched in\n                    <jats:italic>Alistipes<\/jats:italic>\n                    , ST3 in\n                    <jats:italic>Escherichia-Shigella<\/jats:italic>\n                    ). Disease-associated biomarkers included UC-linked depletion of butyrate producers and enrichment of\n                    <jats:italic>Cutibacterium<\/jats:italic>\n                    ,\n                    <jats:italic>Comamonas<\/jats:italic>\n                    , and\n                    <jats:italic>Dialister<\/jats:italic>\n                    ; depletion of\n                    <jats:italic>Clostridia UCG-014<\/jats:italic>\n                    in CD; and enrichment of fermentative fungi (\n                    <jats:italic>Candida<\/jats:italic>\n                    ,\n                    <jats:italic>Meyerozyma<\/jats:italic>\n                    ) and bacteria (\n                    <jats:italic>Coprococcus<\/jats:italic>\n                    ,\n                    <jats:italic>Catenibacterium<\/jats:italic>\n                    ) in IBS. Cross-domain networks were resilient and modular in controls and IBS but fragile in UC and intermediate in CD. These findings highlight trans-kingdom interactions and\n                    <jats:italic>Blastocystis<\/jats:italic>\n                    carriage as ecological features of the gut microbiome in IBS and IBD, with enterotype-succinotype stratification offering complementary biomarkers for disease classification in a non-Western cohort.\n                  <\/jats:p>","DOI":"10.1186\/s13099-026-00819-3","type":"journal-article","created":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T15:04:17Z","timestamp":1775919857000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Bacterial and fungal biomarkers in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD): trans-kingdom interactions, Blastocystis carriage, and enterotype\u2013succinotype stratification"],"prefix":"10.1186","volume":"18","author":[{"given":"Ayman A.","family":"El-Badry","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4770-3929","authenticated-orcid":false,"given":"Abdulaziz A.","family":"Al-Quorain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7056-4023","authenticated-orcid":false,"given":"Nehal","family":"Hosin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1033-1335","authenticated-orcid":false,"given":"Mark","family":"van der Giezen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2109-4344","authenticated-orcid":false,"given":"Yohannes","family":"Seyoum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,11]]},"reference":[{"key":"819_CR1","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. 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