Gut Microbiota

in health & disease

The word 'microbiota' refers to the population of microorganisms that live on or in the human body, including bacteria, archaea, yeast and viruses. 


In the gastrointestinal tract there are at least as many bacterial cells as there are human cells in the whole of the body – this cluster of microorganisms is referred to as the gut microbiota. This vast microbial population is important not just for nutrient digestion but also for health maintenance. Consequently, there is extensive international research into the composition and activity of the gut microbiota and its influence on health.

Gut Health

The gut microbiota & gastrointestinal health

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The gut microbiota & immune health

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Did you know...

The gut microbiota: 

• Weighs about 0.2 kg

• Has a gene set approximately 150 times larger than the human gene set

• Has a genome that is over 99% from bacteria, representing more than 1,000 different species 

• Is individual to you - only about 40% of the genes are shared with any other person

• Distribution is determined by pH, oxygen availability, nutrient availability and transit time

Role of the Gut Microbiota

Although it is not possible to define a healthy gut microbiota, the complex relationship between the number, activity and diversity of both beneficial and harmful bacteria in a healthy intestine is what makes up a balanced gut microbiota.

The gut microbiota plays an important role in many metabolic, nutritional, physiological and immunological processes including;

• Fermentation of non-digestible dietary fibre

• Production of short-chain fatty acids

• Vitamin K2 production

• Prevention of colonisation of pathogenic microorganisms

• Modulation of intestinal epithelial cell proliferation

• Development and homeostasis of the immune system

Factors affecting the Gut Microbiota

Maintaining a balanced gut microbiota is key, as harmful bacteria can have more damaging effects in the gut, such as promoting the formation of carcinogenic substances and producing toxins. Disturbance in the balanced gut microbiota, known as dysbiosis, is associated with several conditions including inflammatory bowel diseases and metabolic diseases, such as diabetes. 


There are a range of factors that affect the composition of the gut microbiota including diet, age, smoking, physical activity, medication and stress.

For example...

Diet: A recent review1 summarised specific foods and dietary patterns that can all influence the abundance and types of bacteria in the gut. For example, human observational and interventional studies have shown that fibre and prebiotic consumption increases microbial diversity and short chain fatty acid production. 

Medication: It is now well known that antibiotic use can rapidly alter the gut microbiota composition, often decreasing bacterial diversity and abundance of bacterial families and genus2. Researchers are now interested in understanding how these changes impact host health3. There is also observational and intervention studies showing evidence that other commonly prescribed medications may also have a notable impact on the gut microbiota including statins, proton-pump inhibitors (PPI), metformin, nonsteroidal anti-inflammatory drugs (NSAID), antipsychotics and opioids4.



1. Valdes et al. (2018) BMJ 361:j2179

2. Langdon et al. (2016) Genome Med. 8:39.

3. Francino (2016) Front Microbiol. 6:1543.

4. Le Bastard et al. (2018) Aliment Pharmacol Ther. 47:332–345