Towards microbial fermentation metabolites as markers for health benefits of prebiotics

Kristin A. Verbeke, Alan R. Boobis, Alessandro Chiodini*, Christine A. Edwards, Anne Franck, Michiel Kleerebezem, Arjen Nauta, Jeroen Raes, Eric A.F. Van Tol, Kieran M. Tuohy

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

137 Citations (Scopus)


Available evidence on the bioactive, nutritional and putative detrimental properties of gut microbial metabolites has been evaluated to support a more integrated view of how prebiotics might affect host health throughout life. The present literature inventory targeted evidence for the physiological and nutritional effects of metabolites, for example, SCFA, the potential toxicity of other metabolites and attempted to determine normal concentration ranges. Furthermore, the biological relevance of more holistic approaches like faecal water toxicity assays and metabolomics and the limitations of faecal measurements were addressed. Existing literature indicates that protein fermentation metabolites (phenol, p-cresol, indole, ammonia), typically considered as potentially harmful, occur at concentration ranges in the colon such that no toxic effects are expected either locally or following systemic absorption. The endproducts of saccharolytic fermentation, SCFA, may have effects on colonic health, host physiology, immunity, lipid and protein metabolism and appetite control. However, measuring SCFA concentrations in faeces is insufficient to assess the dynamic processes of their nutrikinetics. Existing literature on the usefulness of faecal water toxicity measures as indicators of cancer risk seems limited. In conclusion, at present there is insufficient evidence to use changes in faecal bacterial metabolite concentrations as markers of prebiotic effectiveness. Integration of results from metabolomics and metagenomics holds promise for understanding the health implications of prebiotic microbiome modulation but adequate tools for data integration and interpretation are currently lacking. Similarly, studies measuring metabolite fluxes in different body compartments to provide a more accurate picture of their nutrikinetics are needed.

Original languageEnglish
Pages (from-to)42-66
JournalNutrition Research Reviews
Issue number1
Publication statusPublished - 2015


  • Metagenome
  • Microbial metabolites
  • Nutrikinetics
  • Prebiotic health benefits

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