What Is The Gut Microbiota?

  • Eden Mostafa, Integrated Master's, Pharmacy, University of Birmingham
  • Sophie Downton, BSc, Biomedical Sciences, University of Reading


The term 'gut microbiota' refers to all the communities of microorganisms, including bacteria, archaea (primitive bacteria), eukarya (primitive animals), or viruses within our small and large intestines.2 Sometimes termed ‘gut flora' or 'gut microbes', 'Gut microbiomes' are generally defined as the environment of the gut microbiota and their metabolic activities and products. Estimated, the number of cells in bacterial communities in our gastrointestinal tract (GI tract) is over 10 times greater than the number of human cells.

Why do many of these microbes not harm our bodies and cause disease? The answer is that they have lived with us through millions of years of coevolution. The mutualistic relationship between humans and the gut microbiome means that they cannot live without us, and we benefit from their existence in our bodies. Scientists are starting to call the human gut microbiome the ‘essential organ’, after decades of studies of its relationship to the human body.

Functions and roles of gut microbiota

The microbiota regulates numerous metabolic pathways and homeostasis, such as the pH of the gut, which are crucial mechanisms to balance our body’s activities. Those also include supporting the immune system, preventing pathogens such as harmful bacteria from colonising the gut, and shaping the gut structures. When those balances are disturbed, called ‘gut dysbiosis’, it may damage body function and lead to various health conditions.

The main function of the gut microbiota is to interfere with the food and chemical processes in the human gut, including:3,4

  • Fermenting the indigestible fibre in processed foods such as vegetables and producing short-chain fatty acids (SCFAs), which play several roles all over the body.
  • Breaking down potentially toxic food compounds.
  • Synthesise certain vitamins and amino acids, such as vitamin B12, which can only be produced by gut bacteria and not from other food sources.

Commensal, or neutral, gut bacteria are believed to protect our gut health from an overgrowth of harmful bacteria by competing for nutrition. Numerous known bacterial species can be considered ‘good bacteria’ or ‘beneficial bacteria’, however, with a certain amount of balance.

Composition and diversity of gut microbiota

The diversity of the gut microbiota composition is key to gut health. Studies on gut microbiota composition are conducted using genetic sequencing technologies, providing a wide range of data on gut microbiota diversity. When the diversity of the gut microbiota is low, it can indicate gut dysbiosis, which is associated with several diseases.

For example, long-term antimicrobial usage in patients might lead to Clostridium difficile infection in the large bowel, which emerges from diversity disturbance. Commensal bacteria under normal conditions are destroyed by certain antimicrobials, resulting in gut pH imbalance and Clostridium difficile overgrowth. A recently researched treatment for severe cases of Clostridium difficile infection is to rebalance the gut microbiome composition with a procedure called ‘faecal microbiota transplantation’, which can be done by delivering the stool suspension to the patient's large bowel.

Gut microbiota and health

Gut microbiota composition not only affects gut health but is also considered to influence all over our body. The process of maintaining balance in the human body and producing crucial chemicals, such as SCFAs, plays large roles in human health. The following conditions can arise in the case of gut dysbiosis;

  • Metabolic diseases such as obesity, diabetes, or non-alcoholic fatty liver disease are linked with energy metabolism.
  • Gastrointestinal diseases: irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), or even bowel cancer are influenced by chemical processes of the gut microbiome.
  • Cardiovascular diseases: hypertension, blood vessel diseases, or heart disease are connected with the role of SCFAs and several metabolites.
  • Neurodegenerative diseases, such as Parkinson’s disease or Alzheimer’s disease, are significantly associated with the gut-brain axis, the communication via the nervous, endocrine, and immune systems, which are affected by gut microbiota.

Factors affecting gut microbiota

Other than food ingestion, various factors determine human gut microbiota in children and adults.

  • Vaginal birth; compared to caesarean section, vaginal birth promotes the colonisation of gut microbes, affecting the infant’s health and immunity.
  • Breastfeeding: breast milk contains various microorganisms that promote gut microbiomes and stimulate immune cells and the immune system of the infant.
  • Nutrient consumption
    • Types of carbohydrates, proteins, and lipids
    • Fibre consumption, especially in digestive fibre, which is considered to be prebiotic
    • Coffee, tea, or certain minerals can promote gut microbe diversity.
  • Diet choices and patterns that effectively promote gut microbiota
    • Vegetarian or vegan diet
    • Mediterranean diet
    • Ketogenic diet
    • Intermittent fasting

With those factors, we are able to manipulate microbes in our bodies. Some food recommendations are shown to promote higher gut microbe diversity: 

  • Probiotic foods, usually found as fermented foods such as yoghurt, kefir, or pickled vegetables, contain beneficial bacteria or yeasts that are good for gut health. Sometimes, they come in the form of normal food with added probiotics.
  • Probiotic supplements, which are marketed worldwide to deliver ‘healthy’ bacteria to the gut, have conflicting evidence on their efficacy for health. Probiotics may be recommended by a healthcare professional or taken at an individual’s discretion. 
  • Prebiotics are the substances that are consumed by gut bacteria and promote our health. For example, in digestive fibre from various types of food.
  • Synbiotics involves mixing prebiotics and probiotics supplementary to food.

However, the long-term effects of gut microbiota manipulation are still under research, with the association between diet and disease not quite understood.


Gut microbiota is such a complex and astonishing knowledge. This emerging field of life sciences has far more things to be discovered. Getting a healthy gut microbiome is confirmed to be one of the ways to achieve good health; however, eating probiotic cookies every day is far from guaranteeing a healthy life.

The gut microbiota is the term used to describe the total composition of all species of bacteria and bacterial products in the intestinal environment. The association between the gut microbiome and disease is an emerging field of health science that shows great promise for both understanding the onset and treatment of disease. A balanced, healthy gut microbiome is greatly associated with good health, while taking antibiotic medications, even to kill pathogenic bacteria, is associated with the death of our commensal bacteria. A healthy diet is recommended to maintain both intestinal bacterial and system-wide health.


  1. Thursby E, Juge N. Introduction to the human gut microbiota. Biochemical Journal [Internet]. 2017 Jun 1 [cited 2023 Jul 27];474(11):1823–36. Available from: https://portlandpress.com/biochemj/article/474/11/1823/49429/Introduction-to-the-human-gut-microbiota 
  2. Moszak M, Szulińska M, Bogdański P. You are what you eat—the relationship between diet, microbiota, and metabolic disorders—a review. Nutrients [Internet]. 2020 Apr [cited 2023 Jul 28];12(4):1096. Available from: https://www.mdpi.com/2072-6643/12/4/1096
  3. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ [Internet]. 2018 Jun 13 [cited 2023 Jul 27];k2179. Available from: https://www.bmj.com/lookup/doi/10.1136/bmj.k2179 
  4. Avenue 677 Huntington, Boston, Ma 02115. The Nutrition Source. 2017 [cited 2023 Jul 28]. The microbiome. Available from: https://www.hsph.harvard.edu/nutritionsource/microbiome/ 
  5. Baby Friendly Initiative [Internet]. [cited 2023 Jul 29]. Emerging research: Epigenetics and the microbiome. Available from: https://www.unicef.org.uk/babyfriendly/news-and-research/baby-friendly-research/infant-health-research/epigenetics-microbiome-research/ 
This content is purely informational and isn’t medical guidance. It shouldn’t replace professional medical counsel. Always consult your physician regarding treatment risks and benefits. See our editorial standards for more details.

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Pharanyoo Osotthanakorn

Doctor of Medicine (MD), Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Thailand

Peem is a Health policy and systems researcher with an interest in health policy and economics, as well as health education. Peem had a 6-month internship as a research assistant at the Department of Community Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Thailand. Peem has also worked as a web content writer for FitSloth, a health tech startup in Thailand, about personalised nutrition for one year. He is currently a visiting researcher at the Value-Based Health and Care Academy, School of Management, Swansea University, working on research about Value-Based Health Care policy implementation.

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