Dietary carbohydrates impact multiple host systems, including gut functions, the gut microbiome and immunometabolic health. There is great interest in promoting microbial-dependent health benefits through manipulating the carbohydrate profile of food, especially by increasing dietary fibre content. However, microbial and host responses to dietary fibre supplementation show unpredictable interindividual variation. We hypothesise that different types of dietary fibre and the interactive effects with other diet components shape microbial interactions.

To test this hypothesis, we functionally categorised carbohydrates by host- and microbial-accessibility and designed ten carbohydrate profiles by altering the proportions of glucose and sucrose to resistant starch type II and type III to inulin and guar gum. Using a mouse model, we systematically investigated these carbohydrate profiles at two macronutrient compositions (high prot:carb or high carb:prot), and two absorbable energies (high or low levels of indigestible carbohydrates), in a total of 40 experimental diets. Gastrointestinal transit was inferred through faecal and caecal attributes, and the presence of faecal blood was used as an indicator of gut epithelial health. The gut microbiota was analysed by 16S amplicon profiling using faecal samples.

Intake of host-inaccessible microbial-accessible carbohydrates (HI-MAC) was significantly correlated with increased faecal moisture content (p<0.01) and caecal size (p<0.05). Diets with high HI-MAC were also associated with reduced faecal blood. Notably, the same carbohydrate profiles had distinct impacts when diets differed in protein content. The microbial composition was driven by the carbohydrate profile, but the overall outcomes were dependent on the dietary context. The relative abundance of Bifidobacterium increased with high intake of HI-MAC, but only in diets with low protein intake. The microbial interaction network also differed depending on the diet context, with Bifidobacterium as the most interconnected at high carb:prot diets, and Allobaculum at high prot:carb.

We conclude that not only is the type and availability of carbohydrates important, but understanding the interactions between multiple dietary dimensions is essential in predicting microbial responses and health effects.