Bacterial and fungal biomarkers in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD): trans-kingdom interactions, Blastocystis carriage, and enterotype–succinotype stratification

The gut microbiome, encompassing bacteria, fungi, and protists, is integral to gastrointestinal (GI) health and disease. 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’s disease (CD), and controls. Analyses incorporated bacterial enterotypes, succinotypes, and Blastocystis carriage to explore ecological and metabolic stratification. Differences in community composition were largely explained by GI disorder, host factors, enterotype, and Blastocystis carriage, accounting for 1–9% of bacterial and fungal variation. IBS patients exhibited increased bacterial richness and evenness, whereas UC and CD displayed stronger fungal dysbiosis. Enterotyping identified two Bacteroides-dominant clusters: Bact1 (with Faecalibacterium, Alistipes) and Bact2 (enriched in Escherichia-Shigella, Streptococcus), with Bact2 linked to reduced diversity and elevated calprotectin. Succinotyping distinguished Dialister-dominant (D-type) and Phascolarctobacterium-dominant (P-type) communities; UC was enriched in fragile, bridge-dependent D-type networks, in contrast to resilient, short-chain fatty acid (SCFA)- and H2S-producing P-type networks. Blastocystis was detected in 48% of participants (mainly subtypes 1 (ST1) and ST3). It was associated with enrichment of butyrate-producing bacteria (Roseburia, Anaerobutyricum, Butyribacter) and distinct fungal genera, with subtype-specific signatures (ST1 enriched in Alistipes, ST3 in Escherichia-Shigella). Disease-associated biomarkers included UC-linked depletion of butyrate producers and enrichment of Cutibacterium, Comamonas, and Dialister; depletion of Clostridia UCG-014 in CD; and enrichment of fermentative fungi (Candida, Meyerozyma) and bacteria (Coprococcus, Catenibacterium) 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 Blastocystis 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.