Diet rapidly and reproducibly alters the human gut microbiome
Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut1, 2, 3, 4, 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.
Nature Alert Commentary
Diet rapidly and reproducibly alters the human gut microbiomeWe know that diet influences the composition of the gut microbiota in
the long term. Now a study of healthy volunteers switched to either
a plant- or animal-based diet shows that gut microbiome changes
rapidly, overwhelming pre-existing inter-individual differences in
microbiota composition within a single day to produce a gut ecology
typical of herbivorous and carnivorous mammals in general. The
carnivores’ diet was associated with high levels of bile-tolerant
microbes, including the bacterium Bilophila wadsworthia which has
previously been linked to inflammatory bowel disease.