Diet rapidly and reproducibly alters the human gut microbiome

Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.


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.

Publication types

  • Clinical Trial
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Bacteria / drug effects
  • Bacteria / genetics*
  • Bacteria / isolation & purification*
  • Bacteroides / drug effects
  • Bacteroides / genetics
  • Bacteroides / isolation & purification
  • Bile Acids and Salts / analysis
  • Bile Acids and Salts / metabolism
  • Bilophila / drug effects
  • Bilophila / genetics
  • Bilophila / isolation & purification
  • Carnivory
  • Diet* / adverse effects
  • Diet, Vegetarian
  • Dietary Fats / adverse effects
  • Dietary Fats / pharmacology
  • Feces / chemistry
  • Feces / microbiology
  • Female
  • Fermentation / drug effects
  • Food Microbiology
  • Gastrointestinal Tract / drug effects
  • Gastrointestinal Tract / microbiology*
  • Gastrointestinal Tract / virology
  • Gene Expression Regulation, Bacterial / drug effects
  • Herbivory
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Male
  • Metagenome* / drug effects
  • Metagenome* / genetics
  • Microbiota* / drug effects
  • Microbiota* / genetics
  • Time Factors
  • Young Adult


  • Bile Acids and Salts
  • Dietary Fats

Associated data

  • GEO/GSE46761