Long-term diet influences the structure and activity of the trillions of
microorganisms residing in the human gut1–5, but it
remains unclear how rapidly and reproducibly the human gut microbiome responds
to short-term macronutrient change. Here, we show that the short-term
consumption of diets composed entirely of animal or plant products alters
microbial community structure and overwhelms inter-individual differences in
microbial gene expression. The animal-based diet increased the abundance of
bile-tolerant microorganisms (Alistipes, Bilophila, and
Bacteroides) and decreased the levels of Firmicutes that
metabolize dietary plant polysaccharides (Roseburia, Eubacterium
rectale, and Ruminococcus bromii). Microbial
activity mirrored differences between herbivorous and carnivorous
mammals2, reflecting
trade-offs between carbohydrate and protein fermentation. Foodborne microbes
from both diets transiently colonized the gut, including bacteria, fungi, and
even viruses. Finally, increases in the abundance and activity of
Bilophila wadsworthia on the animal-based diet support a
link between dietary fat, bile acids, and the outgrowth of microorganisms
capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the
gut microbiome can rapidly respond to altered diet, potentially facilitating the
diversity of human dietary lifestyles.
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