Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut,
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 mammals,
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
disease.
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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