Prebiotic Modulation of FMT Donor Microbiota

Metabolic dysfunction-associated steatotic liver disease is a prevalent and progressive condition closely linked to gut microbiota composition and function. While fecal microbiota transplantation shows promise in restoring a health-associated microbiome, its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may offer a strategy to selectively support keystone microbes linked to reduced MASLD risk. This study aimed to evaluate the potential of two prebiotics - inulin and xylooligosaccharides - to modulate the microbiota of healthy FMT donors in vitro, with a focus on enriching beneficial bacterial taxa and functions associated with MASLD resilience.Stool samples from eight approved FMT donors were cultured anaerobically for 24 hours in an in vitro gut model, with or without inulin or XOS supplementation. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis.Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides - genera associated with short-chain fatty acid production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional predictions revealed relatively enriched pathways related to carbohydrate metabolism, vitamin biosynthesis (biotin, thiamine, menaquinone, and queuosine), fatty acid metabolism, and tryptophan degradation - many of which are relevant to MASLD pathophysiology. Acetate concentrations were significantly elevated by both prebiotics, while butyrate showed a donor-dependent trend toward increase.Prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting the potential of prebiotics as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.