Gut microbial activity, implications for health and disease: the potential role of metabolite analysis

J Proteome Res. 2012 Dec 7;11(12):5573-85. doi: 10.1021/pr300637d. Epub 2012 Nov 1.


Microbial metabolism of proteins and amino acids by human gut bacteria generates a variety of compounds including phenol, indole, and sulfur compounds and branched chain fatty acids, many of which have been shown to elicit a toxic effect on the lumen. Bacterial fermentation of amino acids and proteins occurs mainly in the distal colon, a site that is often fraught with symptoms from disorders including ulcerative colitis (UC) and colorectal cancer (CRC). In contrast to carbohydrate metabolism by the gut microbiota, proteolysis is less extensively researched. Many metabolites are low molecular weight, volatile compounds. This review will summarize the use of analytical methods to detect and identify compounds in order to elucidate the relationship between specific dietary proteinaceous substrates, their corresponding metabolites, and implications for gastrointestinal health.

Publication types

  • Review

MeSH terms

  • Amino Acids / chemistry
  • Animals
  • Bacteria / chemistry
  • Bacteria / growth & development*
  • Biomarkers / analysis
  • Colorectal Neoplasms / chemistry
  • Colorectal Neoplasms / microbiology
  • Colorectal Neoplasms / pathology
  • Diet, High-Fat / adverse effects
  • Dietary Proteins / adverse effects
  • Feces / chemistry
  • Gastrointestinal Tract / chemistry
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Inflammatory Bowel Diseases / pathology
  • Lipid Metabolism
  • Magnetic Resonance Spectroscopy
  • Metabolome*
  • Metabolomics / methods*
  • Volatile Organic Compounds / analysis
  • Volatile Organic Compounds / chemistry


  • Amino Acids
  • Biomarkers
  • Dietary Proteins
  • Volatile Organic Compounds