Crohn's & colitis 360 · 2026
Microbial predictors of sustained clinical remission following the Crohn's disease exclusion diet in adults and microbiome shifts toward healthy pediatric controls.
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Sigall-Boneh Rotem, Organ Sarah, Ghiboub Mohammed, Yanai Henit, Abramas Lee, Wierdsma Nicolette, Verburgt Charlotte M, de Jonge Wouter J, Derikx Joep P M, Lewis James D, Gu Hong, Bielawski Joseph, Maharshak Nitsan, Dotan Iris, Wine Eytan, Dunn Katherine, Van Limbergen Johan
Аннотация
BACKGROUND: The Crohn's disease (CD) exclusion diet (CDED) is an emerging dietary therapy for inducing remission in CD. However, data on its effects on gut microbiome in adults remain limited. This study investigated microbial responses to CDED in adults with mild-to-moderate CD and compared them with pediatric patients and healthy pediatric controls.
METHODS: Microbiome data were analyzed from a randomized controlled trial (RCT) in adults (baseline, weeks 6, 12, 24) and a pediatric RCT (baseline, weeks 6, 12). Baseline microbial composition, diversity, and functional potential were compared between patients who achieved sustained clinical remission (SCR) at both weeks 12 and 24 and those who did-not. Functional profiling was performed using gene ortholog annotations, linear discriminant analysis, and metabolite inference.
RESULTS: Baseline microbial and functional profiles differed between patients with and without SCR. SCR was associated with lower alpha diversity, higher relative abundances of Alistipes and Faecalibacterium, and increased flagellin gene expression. SCR was associated with enrichment of genes for redox balance, fatty acid metabolism, and DNA repair, while non-SCR showed elevated NAD biosynthesis, bacterial adhesion, and pro-inflammatory pathways. Haemophilus and Prevotella were negatively linked to SCR. Compositional and functional microbiome analyses revealed a microbiome shift during CDED-induced remission toward a profile more similar to healthy pediatric controls.
CONCLUSIONS: Before and during CDED, distinct baseline microbial and functional profiles were associated with SCR. These highlight the potential of the gut microbiome as a biomarker for identifying patients most likely to benefit from sustained effects of dietary therapy, supporting a more personalized approach to CD management.
METHODS: Microbiome data were analyzed from a randomized controlled trial (RCT) in adults (baseline, weeks 6, 12, 24) and a pediatric RCT (baseline, weeks 6, 12). Baseline microbial composition, diversity, and functional potential were compared between patients who achieved sustained clinical remission (SCR) at both weeks 12 and 24 and those who did-not. Functional profiling was performed using gene ortholog annotations, linear discriminant analysis, and metabolite inference.
RESULTS: Baseline microbial and functional profiles differed between patients with and without SCR. SCR was associated with lower alpha diversity, higher relative abundances of Alistipes and Faecalibacterium, and increased flagellin gene expression. SCR was associated with enrichment of genes for redox balance, fatty acid metabolism, and DNA repair, while non-SCR showed elevated NAD biosynthesis, bacterial adhesion, and pro-inflammatory pathways. Haemophilus and Prevotella were negatively linked to SCR. Compositional and functional microbiome analyses revealed a microbiome shift during CDED-induced remission toward a profile more similar to healthy pediatric controls.
CONCLUSIONS: Before and during CDED, distinct baseline microbial and functional profiles were associated with SCR. These highlight the potential of the gut microbiome as a biomarker for identifying patients most likely to benefit from sustained effects of dietary therapy, supporting a more personalized approach to CD management.