Dietary fibre responses in microbiota reveal opportunity for disease-specific prebiotic approaches

Prebiotics or fermentable dietary fibres are known for their potential to shape the gut microbial community and could be used as a tool in treating gut dysbiotic states found in a wide range of diseases. However, it remains unclear whether the microbiota of individuals with distinct diseases respond to fibre treatments in the same way as healthy individuals do. In this study, a mechanistic understanding of fibre responses across health conditions was performed through in vitro faecal fermentations with various dietary fibres and faecal microbial communities from healthy individuals (HC) as well as Crohn's disease (CD), ulcerative colitis (UC), and Parkinson's disease (PD). Production of short chain fatty acids (SCFAs) was measured, and microbial community structure shifts were assessed using 16S rRNA gene amplicon sequencing. All tested dietary fibres increased short chain fatty acid production upon fermentation, with variations based on both, disease state and fibre type. The magnitude of shifts in microbial community structure resulting from in vitro fermentation varied by condition; for example, samples from individuals with UC responded weakly to fibre fermentation, while those from individuals with PD underwent dramatic changes. Still, each health condition had distinct fibre types that were more effective in shifting the community structure and increasing SCFAs. Overall, these results suggest that the response to fibres on gut microbiota varies by disease. The selection of disease-specific prebiotics could be tailored according to health conditions for optimal desired gut microbiota responses.