LAUSR

ident gut microorganisms, termed commensal microbes, can affect human health. Promoting beneficial commensal microbes through a type of nutritional supplement called a prebiotic is an area of intensive scientific and medical research. However, trying to harness a diet with the desired effect is challenging because the gut microbial community (also known as the microbiome) is highly complex, and because dietary responses are modulated by multiple hereditary and non-hereditary factors. Writing in Nature, Delannoy-Bruno et al. fill an essential gap in our mechanistic understanding of diet–microbiome interactions by focusing on dietary fibre, a family of substances of pronounced physiological virtues that are predominantly metabolized by commensal microbes. This provides a sequel to the team’s previous work on the development of microbiome-targeting foods. To characterize the effect of dietary-fibre supplementation in overweight individuals, Delannoy-Bruno and colleagues used germfree mice — animals raised and maintained in a sterile environment that are therefore devoid of the usual resident microbes of any sort. The team colonized the gut of each of nine mouse groups with the microbiome of one of nine women classed as obese. The mice were continuously fed a low-fibre, high-fat diet, coupled with periodic fibre supplementation (Fig. 1). Their microbiome was characterized to assess gene content (the level of particular genes present) before, during and after each episode of fibre supplementation. Building on previous work by this team, which identified fibres that promote the growth of certain intestinal bacteria (those of the genus Bacteroides, which are less prevalent than normal in obese individuals), Delannoy-Bruno et al. chose three types of fibre that were fed sequentially to the mice. Each supplementation cycle was followed by a ‘washout’ period to enable intestinal clearing of the fibres, thereby allowing the authors to discern the effect of every individual type of fibre as distinct from the other fibres. Human-microbiome-inoculated mice showed pronounced compositional shifts in their gut microbes in response to fibre supplementation. To identify fibre–microbe interactions and subtract irrelevant ‘noise’ in the data arising from normal fluctuations in the microbiome profile, the authors used a feature-reduction approach termed higher-order singular value decomposition. This revealed that exposure of the microbial population to a particular fibre resulted in a greater presence of genes that encode proteins needed for the metabolism of that fibre. For example, consumption of cellulose-containing pea and orange fibre led to a higher representation of genes encoding the β-glucosidase enzymes that hydrolyse such fibre, probably owing to the proliferation of bacteria that can use cellulose as an energy source. Interestingly, in mice inoculated with human microbiomes, similar signatures of fibre-responsive genes became highly abundant through the expansion of Microbiology