Gut fungi and bacteria shift together in IBS and IBD, with disease status explaining ~4–9% of microbiome differences and fungal changes often stronger in inflammatory conditions like ulcerative colitis and Crohn’s. People with IBS showed higher bacterial diversity, while IBD cases had more fungal imbalance, including overgrowth of fungi like Candida and loss of beneficial, short-chain fatty acid–producing microbes. A common gut microbe, Blastocystis, appeared in ~48% of people and was linked to higher levels of beneficial bacteria that support digestion, showing fungi can actively reshape gut health, not just reflect it.