Microbiome, Fibre and Fermentation

April 23rd, 2021 | Posted in Info

Each person’s microbiome is highly individual and if you’ve read the blog post Microbiome, Diet and Health you’ll know that what we eat is one of the most important forces shaping the gut microbiota. In as little as 24-hours of dietary changes there may be transient alterations in gut microbial composition. However,  it is our long term, daily, dietary habits that drive the establishment of stable, dominant microbial networks. These networks can be used to classify an individual’s gut bacterial profile and may eventually be used as an indicator of disease risk.

Here we’ll look at the effect of macronutrients and fibre on the microbiome. See blog post on Microbiome, Phytochemicals and Health to find out how specific foods affect the health of the gut and beyond.

Plant-based vs. Animal-based Diets

Whether we eat a largely plant based, high fibre diet or an animal-based diet, higher in fat and protein, appears to be a predictor of the composition and function of our gut microbiome. Numerous studies show that vegetarians compared with omnivores exhibit a lower risk for various chronic diseases including obesity, hypertension, dyslipidaemia, coronary heart disease, stroke, diabetes, and certain cancers. The reasons for this are likely to be complex but it may partly be the lower intakes of fat, dietary cholesterol, and animal proteins among vegetarians. Vegetarians also tend to ingest more fibre, phytochemicals, potassium, magnesium, vitamin C and folate.

Another factor may be that the consumption of a plant-based diet results in distinct gut microbial communities, which in turn, influence processes linked to chronic disease. For example, vegetarians tend to exhibit greater ratios of Prevotella to Bacteroides and greater bacterial diversity than omnivores (1). Having a wide diversity of gut organisms is good for many aspects of health.


Relative to bacteria, humans possess a very limited number of enzymes for the breakdown of dietary carbohydrates. Indigestible components of carbohydrates are defined as dietary fibre. It is fibre that provides the substrate for microbial fermentation in the colon and gives the microbiota their energy. Different types of fibre can only be broken down by specific enzymes made by specific bacteria.

Studies into the effects of different types of fibre on the gut microbiota find that certain fibres increase certain bacteria. For example, galactooligosaccharides, found in human breast milk, have been shown to increase Bifidobacterium.

Inulin is a long chain fructooligosaccharide found in globe artichoke that has been shown to increase Bifidobacterium spp, Lactobacilli/Enterococci, and Atopobium spp and decrease Bacteroides (1).

Whole grains

The human diet rarely includes one type of fibre in isolation, but rather includes a complex mix as a part of the food we eat. Studies involving the consumption of whole grains such as barley, maize and wheat, show them to be bifidogenic in humans meaning they increase the beneficial bifidobacteria. Apples and bananas have a similar effect (1).

Fats and protein

Much research has focussed on the benefits of dietary fibre, which feeds the microbiota. There is also evidence to suggest that dietary fat and protein consumption elicit both compositional and functional changes to the gut microbiome. Some research suggests that protein may lead to potentially harmful by-products that increase the risk of negative health outcomes (2). However, it is not clear cut and it seems that the effects of high protein diets are modulated by factors such as body composition, exercise intensity and the types and amounts of fats consumed (1).

By-Products May Be the Problem

It is not necessarily the organisms themselves that have the biggest effect, but the metabolites produced by the organisms when they ferment fibre that affect health. For example, short chain fatty acids are a by-product of fibre fermentation, and although they are critical to intestinal health and can positively influence host metabolism, they may also contribute to increased energy harvest from the diet (1).


Foods, herbs and dietary supplements are potentially powerful tools to manipulate the composition of the microbiome and thus prevent or treat many diseases.  Further research is needed but the ability to optimise the gut microbiome through dietary strategies could make a big difference to the health of many people.


1. Amy M. Sheflin, Christopher L. Melby, Franck Carbonero & Tiffany L. Weir (2017) Linking dietary patterns with gut microbial composition and function, Gut Microbes, 8:2, 113-129

2. Frame LA et al. Current Explorations of Nutrition and the Gut Microbiome: A Comprehensive Evaluation of the Review Literature. Nutrition Reviews, Oct. 2020; 78, P.798–812,