The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.
Bibliographical noteThis work was conducted by an expert group of the European branch of the International Life Sciences Institute, ILSI Europe. The expert group and this publication was coordinated by the Functional Foods and Prebiotics Task Forces. Industry members of this task force are listed on the ILSI Europe website at http://www.ilsi.eu. Experts are not paid for the time spent on this work; however, the non-industry members within the expert group were offered support for travel and accommodation costs to attend meetings to discuss the manuscript, and a small compensatory sum (honorarium) with the option to decline. The expert group carried out the work, i.e., collecting/analysing data/information and writing the scientific paper separate to other activities of the task forces. The research reported is the result of a scientific evaluation in line with ILSI Europe’s framework to provide a precompetitive setting for public–private partnership (PPP). The opinions expressed herein and the conclusions of this publication are those of the authors and do not necessarily represent the views of ILSI Europe nor those of its member companies. ILSI Europe facilitated scientific meetings and coordinated the overall project management and administrative tasks relating to the completion of this work. In particular, the authors would like to thank Dr. Tobias Recker, Dr. Estefanía Noriega, and Mr. Alex Rankin for their support. Furthermore, the authors would like to thank all participants in the ILSI Europe workshop The Gut Microbiome: Our Misunderstood Friend and Foe (3–4 December 2015, Brussels, Belgium) for their involvement in fruitful scientific discussions and their valuable insights which contributed to the refinement of the draft manuscript.
- gut microbiota
- microbial metabolism
- food components