Predicting a human gut microbiota's response to diet in gnotobiotic mice - PubMed (original) (raw)

Predicting a human gut microbiota's response to diet in gnotobiotic mice

Jeremiah J Faith et al. Science. 2011.

Abstract

The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.

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Figures

Fig. 1

Fig. 1

Total community abundance (biomass) and the abundance of each community member can best be explained by changes in casein. (A) The total DNA yield per fecal pellet increased as the amount of casein in the host diet increased (shown are mean± S.E.M. for each tested concentration of casein). (B) Changes in species abundance as a function of changes in the concentration of casein in the host diet were also apparent for all 10 species; 7 species were positively correlated with casein concentration (e.g., B. caccae) while the remaining three species were negatively correlated with casein concentration (e.g. E. rectale). Data points from the first and second set of mice given the refined diets (see Fig. S1D,E for explanation) are shown in purple and green, respectively, while the mean and standard error for all diets at a given concentration of casein are shown in red and tan, respectively.

Fig. 2

Fig. 2

Mean community member abundance for each diet. The height of each bar indicates the total DNA yield/biomass for a given diet. Casein concentrations (g/kg) for each diet are displayed in gray above each bar. See Fig. S1 and Table S1 for a description of diets A–Q.

Fig. 3

Fig. 3

Example of community member responses to complex human foods. Changes in species abundance as a function of diet ingredients were apparent for all 10 species (Table S9). B. ovatus increased in absolute abundance with increased concentration of oats in the diet (upper panel), while most of the ten bacterial species (including E. rectale and C. aerofaciens; middle and lower panels) responded to multiple ingredients. The mean and standard error for all diets are plotted (no error bars are shown when replicate points are not available). The colored z-axis mesh grid on the 3D plots is a triangle-based linear interpolation of the data with color changes corresponding to the values in the color bar on the right.

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