Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

Abstract

Background: Studies in mice indicate that the gut microbiome influences both sides of the energy-balance equation by contributing to nutrient absorption and regulating host genes that affect adiposity. However, it remains uncertain as to what extent gut microbiota are an important regulator of nutrient absorption in humans.

Objective: With the use of a carefully monitored inpatient study cohort, we tested how gut bacterial community structure is affected by altering the nutrient load in lean and obese individuals and whether their microbiota are correlated with the efficiency of dietary energy harvest.

Design: We investigated dynamic changes of gut microbiota during diets that varied in caloric content (2400 compared with 3400 kcal/d) by pyrosequencing bacterial 16S ribosomal RNA (rRNA) genes present in the feces of 12 lean and 9 obese individuals and by measuring ingested and stool calories with the use of bomb calorimetry.

Results: The alteration of the nutrient load induced rapid changes in the gut microbiota. These changes were directly correlated with stool energy loss in lean individuals such that a 20% increase in Firmicutes and a corresponding decrease in Bacteroidetes were associated with an increased energy harvest of ≈150 kcal. A high degree of overfeeding in lean individuals was accompanied by a greater fractional decrease in stool energy loss.

Conclusions: These results show that the nutrient load is a key variable that can influence the gut (fecal) bacterial community structure over short time scales. Furthermore, the observed associations between gut microbes and nutrient absorption indicate a possible role of the human gut microbiota in the regulation of the nutrient harvest. This trial was registered at clinicaltrials.gov as NCT00414063.

FIGURE 1.

Mean (±SD) food energy content: product label compared with bomb calorimetry. Open columns represent food calories as shown on the product label. Closed columns represent food calories of duplicated meals measured by bomb calorimetry. ***P < 0.0001 (Student's t test).

FIGURE 2.

Study design. Numbers below diet boxes represent study days. WMD, weight-maintaining diet; EXD1, experimental diet 1 representing either 2400 or 3400 kcal/d; EXD2, experimental diet 2 representing either 2400 or 3400 kcal/d; Dye 1, administration of dye 1 (FD&C blue) with food; Dye 2, administration of dye 2 (FD&C blue) with food; Dye 1 in stool, appearance of dye 1 in stool; Dye 2 in stool, appearance of dye 2 in stool; Coll., collection.

FIGURE 3.

UniFrac analysis of the fecal microbiota of lean and obese individuals fed a 2400- or 3400-kcal/d diet. Unweighted UniFrac clustering was used to measure shared phylogenetic diversity. A radial tree was constructed with FigTree (http://tree.bio.ed.ac.uk/software/figtree/). Black bars indicate samples taken from the same individual; colors indicate samples taken from lean (red) or obese (blue) individuals. Purple represents a sample from an individual with a BMI (in kg/m²) of 26.1 who was included in the lean group in Table 1. Black circles on the nodes indicate a confidence level ≥0.7 (jackknife resampling was used to determine a confidence between 0 and 1). Southwestern diet label (SWDL) numbers represent samples collected during different diets (see supplemental Table S7 under “Supplemental data” in the online issue).

FIGURE 4.

Associations between the relative abundance of the 2 dominant bacterial phyla in the distal gut and nutrient load. Associations are shown between changes in the relative abundance of Firmicutes and Bacteroidetes from a weight-maintaining diet (WMD) and food energy content as a percentage of individual [n = 20 (diamonds)] weight-maintaining energy needs (%WMEN) with each experimental diet [2400-kcal/d diet (A and B); 3400-kcal/d diet (C and D)]. For 2 individuals, data for only one experimental diet were available. P and r values were derived from Pearson correlations; P values in parentheses were derived from multiple regression models adjusted for diet order.

FIGURE 5.

Associations between nutrient absorption (stool calories) and phylum-level changes in the fecal bacterial community structure. Changes in Firmicutes (A) and Bacteroidetes (B) between the first weight-maintaining diet and either the 2400- or 3400-kcal/d diet were associated with nutrient absorption on either experimental diet (2400 or 3400 kcal/d) [n = 12, with 2 data points (diamonds) for each individual]. For one individual, data for only the 2400-kcal/d diet were available. P and r values were derived from Spearman's correlations; P values in parentheses were derived from mixed models to account for repeated measures and were adjusted for diet order.

FIGURE 6.

Mean (±SD) changes in energy content in feces between experimental diets. Changes in energy content in feces are shown between the 3400- and 2400-kcal/d diets in lean (n = 11) and obese individuals (n = 8). *P < 0.05 (paired t test). For one lean individual and one obese individual, data were available for only one of the experimental diets; thus, these individuals were excluded from this analysis.