There is growing recognition of the role of diet and other environmental factors in modulating the composition and metabolic activity of the human gut microbiota, which in turn can impact health. This narrative review explores the relevant contemporary scientific literature to provide a general perspective of this broad area. Molecular technologies have greatly advanced our understanding of the complexity and diversity of the gut microbial communities within and between individuals. Diet, particularly macronutrients, has a major role in shaping the composition and activity of these complex populations. Despite the body of knowledge that exists on the effects of carbohydrates there are still many unanswered questions. The impacts of dietary fats and protein on the gut microbiota are less well defined. Both short- and long-term dietary change can influence the microbial profiles, and infant nutrition may have life-long consequences through microbial modulation of the immune system. The impact of environmental factors, including aspects of lifestyle, on the microbiota is particularly poorly understood but some of these factors are described. We also discuss the use and potential benefits of prebiotics and probiotics to modify microbial populations. A description of some areas that should be addressed in future research is also presented.

Objective: A low FODMAP (Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols) diet reduces symptoms of IBS, but reduction of potential prebiotic and fermentative effects might adversely affect the colonic microenvironment. The effects of a low FODMAP diet with a typical Australian diet on biomarkers of colonic health were compared in a single-blinded, randomised, cross-over trial. Design: Twenty-seven IBS and six healthy subjects were randomly allocated one of two 21-day provided diets, differing only in FODMAP content (mean (95% CI) low 3.05 (1.86 to 4.25) g/day vs Australian 23.7 (16.9 to 30.6) g/day), and then crossed over to the other diet with ≥21-day washout period. Faeces passed over a 5-day run-in on their habitual diet and from day 17 to day 21 of the interventional diets were pooled, and pH, short-chain fatty acid concentrations and bacterial abundance and diversity were assessed. Results: Faecal indices were similar in IBS and healthy subjects during habitual diets. The low FODMAP diet was associated with higher faecal pH (7.37 (7.23 to 7.51) vs 7.16 (7.02 to 7.30); p=0.001), similar short-chain fatty acid concentrations, greater microbial diversity and reduced total bacterial abundance (9.63 (9.53 to 9.73) vs 9.83 (9.72 to 9.93) log ₁₀ copies/g; p<0.001) compared with the Australian diet. To indicate direction of change, in comparison with the habitual diet the low FODMAP diet reduced total bacterial abundance and the typical Australian diet increased relative abundance for butyrate-producing Clostridium cluster XIVa (median ratio 6.62; p<0.001) and mucus-associated Akkermansia muciniphila (19.3; p<0.001), and reduced Ruminococcus torques . Conclusions: Diets differing in FODMAP content have marked effects on gut microbiota composition. The implications of long-term reduction of intake of FODMAPs require elucidation. Trial registration number: ACTRN12612001185853.

Very low-carbohydrate diets are often used to promote weight loss, but their effects on bowel health and function are largely unknown. We compared the effects of a very low-carbohydrate, high-fat (LC) diet with a high-carbohydrate, high-fibre, low-fat (HC) diet on indices of bowel health and function. In a parallel study design, ninety-one overweight and obese participants (age 50·6 (sd 7·5) years; BMI 33·7 (sd 4·2) kg/m²) were randomly assigned to either an energy-restricted (about 6–7 MJ, 30 % deficit) planned isoenergetic LC or HC diet for 8 weeks. At baseline and week 8, 24 h urine and faecal collections were obtained and a bowel function questionnaire was completed. Compared with the HC group, there were significant reductions in the LC group for faecal output (21 (sd 145) v. − 61 (sd 147) g), defecation frequency, faecal excretion and concentrations of butyrate ( − 0·5 (sd 10·4) v. − 3·9 (sd 9·7) mmol/l) and total SCFA (1·4 (sd 40·5) v. − 15·8 (sd 43·6) mmol/l) and counts of bifidobacteria (P < 0·05 time × diet interaction, for all). Urinary phenols and p-cresol excretion decreased (P ≤ 0·003 for time) with no difference between diets (P ≥ 0·25). Faecal form, pH, ammonia concentration and numbers of coliforms and Escherichia coli did not change with either diet. No differences between the diets were evident for incidences of adverse gastrointestinal symptoms, which suggests that both diets were well tolerated. Under energy-restricted conditions, a short-term LC diet lowered stool weight and had detrimental effects on the concentration and excretion of faecal SCFA compared with an HC diet. This suggests that the long-term consumption of an LC diet may increase the risk of development of gastrointestinal disorders.

The inactivation of starch branching IIb (SBEIIb) in rice is traditionally associated with elevated apparent amylose content, increased peak gelatinization temperature, and a decreased proportion of short amylopectin branches. To elucidate further the structural and functional role of this enzyme, the phenotypic effects of down-regulating SBEIIb expression in rice endosperm were characterized by artificial microRNA (amiRNA) and hairpin RNA (hp-RNA) gene silencing. The results showed that RNA silencing of SBEIIb expression in rice grains did not affect the expression of other major isoforms of starch branching enzymes or starch synthases. Structural analyses of debranched starch showed that the doubling of apparent amylose content was not due to an increase in the relative proportion of amylose chains but instead was due to significantly elevated levels of long amylopectin and intermediate chains. Rices altered by the amiRNA technique produced a more extreme starch phenotype than those modified using the hp-RNA technique, with a greater increase in the proportion of long amylopectin and intermediate chains. The more pronounced starch structural modifications produced in the amiRNA lines led to more severe alterations in starch granule morphology and crystallinity as well as digestibility of freshly cooked grains. The potential role of attenuating SBEIIb expression in generating starch with elevated levels of resistant starch and lower glycaemic index is discussed.

The metabolic end products of the large bowel microbiota contribute significantly to human health. After weaning to solid foods, some of the most important of these are the short chain fatty acids (SCFA) produced by the fermentation of undigested dietary components and endogenous secretions. The main SCFA are acetate, propionate and butyrate which have numerous documented effects promoting large bowel function. Of the major acids, butyrate seems especially important. It is a major metabolic fuel for colonocytes and promotes a normal phenotype in these cells, potentially lowering the risk of diseases such as colo-rectal cancer. Imbalances in the microbiota are thought to predispose to large bowel dysfunction and probiotics are being developed to correct this. However, most commercial products contain bacteria (lactobacilli and bifidobacteria) which are dominant species in milk-fed infants but have limited roles in adults. Prebiosis is defined usually by the specific stimulation of these bacteria. However, the end products of most probiotics do not include butyrate or propionate which raises questions about their effectiveness in promoting bowel health in adults. Resistant starch (RS) is a dietary fibre component and its fermentation generally favours butyrate production. Dietary RS intakes and faecal butyrate levels are high in populations at low risk of diet-related large bowel diseases. Conversely, RS intakes and faecal butyrate levels are very low in high risk groups. This raises the possibility that greater RS consumption could be of health benefit. RS is not regarded widely as a prebiotic but (according to the accepted definition) most forms show the requisite features in stimulating specific bacteria, giving raised total SCFA and butyrate levels and a consequent benefit to the host. Current efforts to improve public health through increasing RS consumption could be facilitated by greater recognition of its prebiotic role.