Diet, fermentation and the gut microbiota


Daniel So - Research Dietitian and PhD Candidate, 26 February 2018

The previous blogs in this series have provided an overview of the gut microbiota and its various functions. This entry will take a closer look at how fermentation drives the relationship between diet and the gut microbiota.

Fermentation is defined as the breakdown of substances in the absence of oxygen and occurs in the colon, an oxygen-free environment where most of the gut bugs reside (1). The substances fermented are compounds that have escaped digestion in the upper gastrointestinal tract, typically as a result of either poor digestion, excess consumption, or simply because our bodies just aren’t capable of digesting them (2). These substances are predominantly dietary fibre and protein, but also includes other compounds such as fat and polyphenols (3). 

Once in the colon, these substances are exposed to the gut microbiota. Some of these microbes are capable of breaking down these compounds, releasing energy and nutrients into the colonic environment (2). This drives their metabolic activity and fuels their growth, supporting the overall microbial population and producing a range of by-products for our body or other microbes to use (4, 5).

The type of by-product produced depends on type of substance fermented. These by-products can be either:

  • Beneficial, such as include short-chain fatty acids (predominantly acetate, propionate and butyrate), vitamins (mainly vitamin K and B-group vitamins and vitamin K);

  • Benign or generally harmless, such as gases (such as carbon dioxide, hydrogen, hydrogen sulphide and methane); or

  • Potentially harmful, such as ammonia and phenols (6).

Importantly, and as discussed in last week’s blog post, fermentation of carbohydrates and carbohydrate-based substances (such as fibre) typically leads to production of beneficial and benign by-products, whereas protein fermentation is associated with the production of potentially harmful by-products (6, 7). 

Take home messages

Carbohydrate fermentation can be a mutually beneficial process for both the human host and gut microbiota. We never really eat for just one – our trillions of little friends get fed with every bite. A balanced and nutritious diet with a good dose of fibre will keep everyone happy!


1.    Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiological reviews 2010;90(3):859-904. doi: 10.1152/physrev.00045.2009.

2.    El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nature reviews Microbiology 2013;11(7):497-504. doi: 10.1038/nrmicro3050.

3.    Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nature reviews Gastroenterology & hepatology 2017;14(8):491-502. doi: 10.1038/nrgastro.2017.75.

4.    Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Applied and environmental microbiology 2004;70(10):5810-7. doi: 10.1128/aem.70.10.5810-5817.2004.

5.    Ohman L, Tornblom H, Simren M. Crosstalk at the mucosal border: importance of the gut microenvironment in IBS. Nature reviews Gastroenterology & hepatology 2015;12(1):36-49. doi: 10.1038/nrgastro.2014.200.

6.    Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, et al. The gut microbiota and host health: a new clinical frontier. Gut 2016;65(2):330-9. doi: 10.1136/gutjnl-2015-309990.

7.    Windey K, De Preter V, Verbeke K. Relevance of protein fermentation to gut health. Molecular nutrition & food research 2012;56(1):184-96. doi: 10.1002/mnfr.201100542.

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