Modulating the structure and function of the human gut microbiota through diet: a metagenomics insight

The human gut microbiota has evolved in close partnership with host physiology and immune function. Although genetics plays some role in gut microbiota phylogenetic structure, environmental influences appear to govern the successional development of the gut microbiota from low species diversity in early life to the climax microbial communities in adulthood and gut microbiota senescence in old age. Of the environmental influences, diet not only determines community structure in terms of microbial relative abundance but may also determine species presence and absence, and how their functional activities impact on host health. Recent metagenomic studies from populations with very different habitual diets and living in very different regions of the world, have shown that diet, especially the relative proportions of whole plant foods, dietary fiber and polyphenols on the one hand, and refined carbohydrates, sugars, animal protein and fat on the other, can drive very distinct gut microbiota profiles, and that these divergent community structures impact on host:microbiota metabolic and immunological interactions influencing the risk of human disease (Fava et al., 2006; Tuohy et al., 2009, Conterno et al., 2011). De Filippo et al (2010) showed that the gut microbiota of children growing up in rural Burkina Faso following a low energy, high whole plant food, traditional African diet differed markedly from children growing up in urban Florence following a typical modern, Western style diet. Our more recent observations confirm the impact of dietary change or urbanisation on gut microbiota structure and also on the functional potential of the gut microbiome, with major differences in KEGG modules between African and European children. These differences appear to be driven largely by dietary fiber and animal protein/fat. We know from animals studies that fermentable fiber and prebiotics reduce the risk of metabolic disease and obesity (Arora et al., 2012), and similarly, that the type and quantity of both carbohydrate and fat in human diets can impact on microbiota composition and activity (Fava et al., 2012), implicating diet as a major driver of the aberrant gut microbiome associated with obesity and the diseases of obesity. These and similar observations raise the intriguing possibility that chronic human disease associated with overweight and obesity may be modulated by dietary supplementation with these functional foods (Conterno et al, 2011). Similarly, modulation of the gut microbiota impacts on microbial cross-talk with the mammalian immune system. In a collaborative study with the University of Reading, we have shown that dietary supplementation with the synbiotic (Bifidobacterium longum bv. infantis CCUG 52486 and glucooligosaccharides) reduces the severity of flue like symptoms in both the elderly and young adults. Moreover, using metagenomics we have shown that gut microbiota profiles differs significantly with age and that response to flue vaccine may in fact be reflected in gut microbial phylogenetic profiles. If microbiota profiles can be correlated directly with immune response, for example to vaccines or infections, then dietary modulating of these microbiota profiles e.g. using probiotics or prebiotics may also constitute a realistic and versatile population based strategy for reducing the risk and/or severity of important human infections like influenza