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2 Gut microbiota and the gut-brain axis The human gastrointestinal tract is colonized by a dense and diverse community of microorganisms—including bacteria, viruses, fungi, and archaea—collectively known as the gut microbiota ( The initiation of intestinal immune imbalance in IBD is driven by a profound ecological shift away from microbial “tolerance.” Under healthy conditions, the microbiota maintains homeostasis through the production of short-chain fatty acids (SCFAs), particularly butyrate, which promote the differentiation of anti-inflammatory regulatory T cells (Treg) and suppress pro-inflammatory Th1 and Th17 cell maturation ( Faecalibacterium , Roseburia ) leads to a loss of this “immunological brake” (Góralczyk-Bińkowska et al., 2022