Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in 4 days: a pilot study

Nutr Res. 2020 May:77:62-72. doi: 10.1016/j.nutres.2020.03.005. Epub 2020 Mar 26.


Diets rich in animal source foods vs plant-based diets have different macronutrient composition, and they have been shown to have differential effects on the gut microbiome. In this study, we hypothesized that diets with very different nutrient composition are able to change gut microbiome composition and metabolites in a very short period. We compared a fast food (FF) diet (ie, burgers and fries) with a Mediterranean (Med) diet, which is rich in vegetables, whole grains, olive oil, nuts, and fish. Ten healthy subjects participated in a controlled crossover study in which they consumed a Med diet and FF diet in randomized order for 4 days each, with a 4-day washout between treatments. Fecal DNA was extracted and the 16S V4 region amplified using polymerase chain reaction followed by sequencing on an Illumina MiSeq. Plasma metabolites and bile acids were analyzed using liquid chromatography-mass spectrometry. Certain bile-tolerant microbial genera and species including Collinsella, Parabacteroides, and Bilophila wadsworthia significantly increased after the FF diet. Some fiber-fermenting bacteria, including Lachnospiraceae and Butyricicoccus, increased significantly after the Med diet and decreased after the FF diet. Bacterially produced metabolites indole-3-lactic acid and indole-3-propionic acid, which have been shown to confer beneficial effects on neuronal cells, increased after the Med diet and decreased after the FF diet. Interindividual variability in response to the treatments may be related to differences in background diet, for example as shown by differences in Bilophila response in relationship to the saturated fat content of the baseline diet. In conclusion, an animal fat-rich, low-fiber FF diet v. a high-fiber Med diet altered human gut microbiome composition and its metabolites after just 4 days.

Keywords: Bile acids; Biogenic amines; Fast food diet; Gut microbiome; Mediterranean diet.

Publication types

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

MeSH terms

  • Adolescent
  • Adult
  • Bacteria / classification
  • Bacteria / isolation & purification
  • Bile Acids and Salts / blood
  • Biogenic Amines / blood
  • Cross-Over Studies
  • Diet*
  • Diet, Mediterranean*
  • Fast Foods*
  • Feces / microbiology
  • Gastrointestinal Microbiome*
  • Humans
  • Phylogeny
  • Pilot Projects
  • Tryptophan / metabolism*
  • Young Adult


  • Bile Acids and Salts
  • Biogenic Amines
  • Tryptophan