Diet rapidly and reproducibly alters the human gut microbiome.

TitleDiet rapidly and reproducibly alters the human gut microbiome.
Publication TypeJournal Article
Year of Publication2014
AuthorsDavid, LA, Maurice, CF, Carmody, RN, Gootenberg, DB, Button, JE, Wolfe, BE, Ling, AV, A Devlin, S, Varma, Y, Fischbach, MA, Biddinger, SB, Dutton, RJ, Turnbaugh, PJ
Date Published2014 Jan 23
KeywordsAdult, Bacteria, Bacteroides, Bile Acids and Salts, Bilophila, Carnivory, Diet, Diet, Vegetarian, Dietary Fats, Feces, Female, Fermentation, Food Microbiology, Gastrointestinal Tract, Gene Expression Regulation, Bacterial, Herbivory, Humans, Inflammatory Bowel Diseases, Male, Metagenome, Microbiota, Time Factors, Young Adult

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.

Alternate JournalNature
PubMed ID24336217
PubMed Central IDPMC3957428
Grant ListDK0046200 / DK / NIDDK NIH HHS / United States
P30 DK034854 / DK / NIDDK NIH HHS / United States
P50 GM068763 / GM / NIGMS NIH HHS / United States
P50 GM068763 / GM / NIGMS NIH HHS / United States