The human gut microbiota composition and metabolic activities are modulated by the diet, and reciprocally, host metabolism and metabolites also interact with the gut microbiota and diet, shaping a complex interacting network that relates to gut health. Several factors can influence the human gut microbiota, with diet being a very important one. Not only dietary pattern (vegetarian vs. omnivorous dietary pattern) and specific foods are involved, but also food constituents (e.g. fibre provides substrates for intestinal microbial metabolism) and food-associated commensal microbes.

A recent review, led by Dr. Petra Louis from The Rowett Institute at the University of Aberdeen (United Kingdom), explores the evidence that exists for how dietary modulation of gut microbiota composition occurs, and the extent to which it depends on inter-individual microbiota variation in humans.

The authors started the review by pointing out that a change in dietary intake over a period of 2-3 days is enough for enriching not only gut microbiota composition with different species, but also overall gut microbiota diversity. Beyond specific changes led by non-digestible (ND) carbohydrates, the dietary intake of protein, fat and overall carbohydrates is relevant to wide ranging shifts in microbial community composition. As previously reported, long-term dietary habits may lead to different states of the gut microbiota diversity, with Prevotella-dominant gut microbiota in people consuming a plant-based diet and Bacteroides-dominant gut microbiota in those with higher protein and fat intake. However, inter-individual variation in gut microbiota composition before a dietary intervention may also affect responses in terms of both gut metabolites and microbiota composition.

When focusing on changes in microbial community composition in response to variations in dietary substrates, non-digestible (ND) carbohydrates were reported as beneficial for gut microbial growth, whereas phytochemicals and dietary fats-via bile salt biotransformations carried out by specific intestinal bacteria through activation of certain nuclear receptors and G-protein coupled receptors- were reported as selective inhibitors of bacterial groups. Specifically, there are specialized species (called ‘keystone species’) able to degrade ND carbohydrates that have profound influence on other members of the community, therefore allowing a metabolite cross-feeding that determines a highly efficient recovery of energy from fibre. For instance, Bifidobacterium adolescentis and Ruminococcus bromii are considered ‘keystone’ starch-degrading species and could explain inter-subject variations in the response to resistant starch. Gary D. Wu et al. were the first to introduce the idea of ‘permissive’ and ‘restrictive’ gut microbial communities as a possible explanation for differences in responsiveness to increased fibre intake in different human populations.

Dietary fibre intake may mediate shifts of gut microbiota composition in humans and this can be achieved via direct microbial growth stimulation or by increasing fermentation or increasing gut transit, which in turn may affect absorption and colonic pH. Indeed, colonic transit has been shown to be strongly associated with the gut microbial composition, diversity and metabolism, therefore contributing to explanations of inter-individual differences in faecal microbiota composition.

Diet-mediated changes in both microbiota composition and host-derived compounds may determine the impact of diet upon the microbial metabolome. When studying changes in microbial community composition resulting from dietary change, it should be taken into account that absolute population levels estimated by techniques such as fluorescent in situ hybridisation (FISH) provides more relevant data for understanding metabolite formation. By contrast, relative changes reported by sequence-based community analyses are markedly affected by several factors and are not necessarily reflective of changes in numbers of specific microbial groups.

In conclusion, diet plays an important role in shaping the gut microbiota, both in the short and long-term. Although factors involved in inter-individual microbiota variation before a dietary intervention are not yet fully understood, host genotype, early colonisation, environmental acquisition, disease states, and medication are considered relevant to the baseline microbiota.




Flint HJ, Duncan SH, Louis P. The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol. 2017; 38:59-65. doi: 10.1016/j.mib.2017.04.005.