Dose-dependent effects of enteral nutrition on the faecal microbiota and diet-related bacterial metabolites
Introduction: Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact different doses on EN may have on the gut microbiome remains unknown. Methods: Healthy adults replaced all (100% EN) or part (85% EN, 50% EN and 20% EN) of their energy requirements with a fibre, gluten, and lactose-free formula for 7 days. Faecal samples were collected before and on day 7 of each intervention. Faecal pH, water content, short chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and 16S rRNA sequencing were performed. Dietary assessment was performed with 7-day estimated weight food diaries.  Results: Sixty-one participants (31 females; median (IQR) age: 24.7 (23.0-27.8) years) were recruited. A dose-dependent impact of EN on faecal microbiota, diet-related bacterial metabolites (SCFAs/BCFAs) and faecal pH was observed, with changes detectable at EN intakes exceeding 50% of requirements. 100% and 85% EN reduced the abundance of major fibre-fermenting taxa such as Agathobacter, Faecalibaterium, Bifidobacterium and Ruminonoccaceae. In parallel, potentially harmful organisms like Klebsiella, Escherichia-Shigella and Erysipelatoclostridium increased. In the 50% EN group, adherence to a diet high in fish, vegetables, potatoes, non-alcoholic beverages, and fat spreads, and low in cereal products, milk, and meat negatively correlated with changes in microbiota structure (r=-0.75, P=0.025). Conclusions: EN detrimentally influences the faecal microbiota and diet-related bacterial metabolites of healthy individuals in a dose-dependent manner, particularly at doses of at least 50%. The findings of this study have implications for the dietary management and counselling of patients receiving high volume EN.