Metabolic cascades drive spatial prebiotic fermentation in a defined gut consortium

Dietary fiber deficiency shifts the gut microbiota to degrade host mucus, compromising intestinal homeostasis. Mechanistically linking in vitro metabolic dynamics of fiber degradation to in vivo outcomes remains challenging due to a lack of representative model systems. Introducing spatial mucin structures to a defined Oligo-Mouse-Microbiota (OMM12) in vitro consortium allowed us to recapitulate the spatio-temporal dynamics of xylooligosaccharide (XOS) processing in gnotobiotic mice. XOS supplementation rapidly established a stable community state in vitro and in vivo across compositional, metabolic and transcriptional levels. XOS supplementation established distinct functional guilds: Bifidobacterium animalis and Blautia coccoides partitioning xylose and arabinose catabolism, whilst profiting from XOS degradation by Bacteroides caecimuris. Along the colonic axis, a spatial XOS gradient exposes Bl. coccoides's substrate preference for xylose and drives longitudinal functional adaptations. Altogether, our predictive platform proves that regional microenvironments govern prebiotic efficacy, highlighting spatial cascades as essential parameters for targeted microbiome interventions.