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The human colonic microbiome includes all microorganisms inhabiting the colon (including bacteria, fungi, viruses, and parasites).[1,2] Colon microbiome research has focused largely on trying to find a “normal” bacterial microbiome and identify deviations that might be responsible for clinical disease.[1,2] Researchers have discovered that healthy patients can have very different patterns of microbiota. In other words, there is no “normal” microbiome.[1,2] Despite the variations in microbiota between healthy patients, the functions performed by bacteria remain relatively consistent. One of the major functions of the microbiome is to produce Short-Chain Fatty Acids (SCFAs) through the fermentation of undigested starches, fibre or proteins.[2,3] The effects that SCFAs have on many biological processes depend on what has been fermented.[2]

There are two classes of SCFAs produced in the breakdown and fermentation of undigested starches, fibre or proteins. The first is beneficial (fibre-derived) SCFAs and the second is putrefactive (protein-derived) SCFAs.

Beneficial (fibre-derived) SCFAs

Humans lack enzymes to adequately break down many types of dietary fibres.[4,5] Fibres that are considered readily fermentable by bacteria are inulin, wheat dextrin, oligosaccharides, resistant starches, beta-glucan (e.g., oats, barley) and raw guar gum.6 When they enter the colon, these fibres are fermented by colonic bacteria to produce SCFAs.[4] Fibres that are fermented by colonic bacteria are known as prebiotics, although not all fibers act as prebiotics.[7]

Acetate, propionate and butyrate are SCFAs derived from fermentable fibre, and are produced in a ratio of approximately 60:20:20. However, this ratio can be modified by changing the diet.[1,5,8] For example, adding more resistant starch can increase the proportion of butyrate.[9]

A primary role of SCFAs, and butyrate in particular, is to help nourish the cells that line the colon, but emerging research suggests that SCFAs are involved in numerous biochemical signaling processes throughout the body.[4,8] For example, SCFAs have shown immune-modulating, anti-inflammatory and anti-proliferative properties and may reduce the risk of inflammatory diseases, type 2 diabetes, obesity, heart disease and other conditions.[4] It is clear that SCFAs play a role in many physiological processes and may be important markers for many diseases and conditions.[4,5]

Putrefactive (protein-derived) SCFAs

The amount of protein that reaches the colon depends on the protein content of foods consumed, and the digestibility of the protein ingested.[3] Protein fermentation tends to take place after available fibre has been depleted.[3] The resulting protein-derived SCFAs, may be implicated in colorectal cancer and inflammatory bowel disease.[3,4] These protein-derived putrefactive SCFAs are not produced by human enzymes, which make them important markers for bacterial fermentation of protein.[4] Putrefactive SCFAs also produce fermentation byproducts that may contribute to potential other harmful effects within the body.[3]


  1. Clarke G, et al. Minireview: Gut microbiota: the neglected endocrine organ. Mol Endocrinol. 2014 Aug;28(8):1221-38.
  2. Young V. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017 Mar;15:1-14.
  3. Windey K, et al. Relevance of protein fermentation to gut health. Mol Nutr Food Res. 2012 Jan;56(1):184-96.
  4. Koh A, et al. From dietary fibre to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016 Jun 2;165(6):1332-1345.
  5. den Besten G, et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013 Sep;54(9):2325-40.
  6. McRorie J. Evidence-based approach to fibre supplements and clinically meaningful health benefits, Part 1. Nutr Today. 2015 Mar;50(2):82-89.
  7. Slavin J, et al. Fibre and prebiotics: mechanisms and health benefits. Nutrients. 2013 Apr 22;5(4):1417-35.
  8. Wong J, et al. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol. 2006 Mar;40(3):235-43.
  9. Sajilata M, et al. Resistant starch—a review. Compr Rev Food Sci Food Saf. 2006 Jan;5:1-17.

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