2.1 Metabolic – digestion of food

The microorganisms of the gut microbiome play an important role in several metabolic processes – that is, the chemical processes that take place in an organism to produce energy or resources necessary for life.

The breaking down, or digestion, of the food we eat is an important metabolic process, as it enables us to gain energy and nutrients from food. The energy obtained from food is used as fuel by the cells throughout the body, while the nutrients are used as building blocks to manufacture important molecules.

Food is digested within the human gut via several mechanical and chemical processes, and involves many specialised molecules, called enzymes. Once broken down into smaller components, the nutrient molecules cross the gut wall and enter the bloodstream to travel around the body to where they are needed. However, certain substances cannot be digested by the human host.

While most of the digestion by the human host takes place in the stomach and small intestines, a small proportion of the food will not have been fully digested by the time it reaches the large intestine. Here, the microbiota of the microbiome produce their own enzymes which digest some of the remaining food products, particularly complex carbohydrates and dietary fibre, but also some protein and fats. The nutrients from these substances are then absorbed across the gut wall of the human host or used by the bacteria of the microbiome as a food source.

The digestion of dietary fibre by the microbiome is particularly important, as a group of important molecules are produced as a by-product. These molecules are known as short-chain fatty acids (SCFAs) and are absorbed into the human body (Figure 7) where they have several important functions.

As well as producing molecules of use to the human host, some of the bacteria in the microbiome will use the fibre from the diet as their own food source. A lack of fibre can result in some bacterial groups dying out due to a lack of nutrients, leading to an imbalance in the diversity of the microbiota. This is one of the reasons having a diet high in fibre is important for maintaining good health. One type of Firmicutes bacteria, called Lactobacillus, is particularly important for digesting dietary fibre to produce SCFAs (and vitamins). Lactobacillus bacteria are found in high proportions in fermented food, such as kimchi, sauerkraut, yoghurt, and kefir, and in many probiotics (you will learn about probiotics at the end of this course).