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What Is the Gut Microbiome?

BSc in Human Nutrition. PhD in Nutrition and Microbiology.

Writer: Dr. Ruairi Robertson, PhD

BSc in Human Nutrition. PhD in Nutrition and Microbiology.


There is more bacteria in your gut than in all the cells in your body.(P1)

**This article was originally published on healthline on the 27th of June 2017 under the title “What is the Gut Microbiome?” It written by Ruairi Robertson, PhD.

Your body is full of trillions of bacteria, viruses and fungi. They are collectively known as the microbiome. While some bacteria are associated with disease, others are actually extremely important for your immune system, heart, weight and many other aspects of health.

This article serves as a guide to the gut microbiome and explains why it’s so important for your health.


Most of the bacteria can be found in your large intestine (P2)

What is the Gut Microbiome?

Bacteria, viruses, fungi and other microscopic living things are referred to as microorganisms, or microbes, for short.

Trillions of these microbes exist mainly inside your intestines and on your skin.

Most of the microbes in your intestines are found in a “pocket” of your large intestine called the cecum, and they are referred to as the gut microbiome.

Although many different types of microbes live inside you, bacteria are the most studied.

In fact, there are more bacterial cells in your body than human cells. There are roughly 40 trillion bacterial cells in your body and only 30 trillion human cells. That means you are more bacteria than human. (1, 2)

What’s more, there are up to 1,000 species of bacteria in the human gut microbiome, and each of them plays a different role in your body. Most of them are extremely important for your health, while others may cause disease. (3)

Altogether, these microbes may weigh as much as 2–5 pounds (1–2 kg), which is roughly the weight of your brain. Together, they function as an extra organ in your body and play a huge role in your health. 

Good bacteria

Our body is dependent on good bacteria to function well (P3)

How Does It Affect Your Body?

Humans have evolved to live with microbes for millions of years. During this time, microbes have learned to play very important roles in the human body. In fact, without the gut microbiome, it would be very difficult to survive.

The gut microbiome begins to affect your body the moment you are born.

You are first exposed to microbes when you pass through your mother’s birth canal. However, new evidence suggests that babies may come in contact with some microbes while inside the womb. (4, 5, 6)

As you grow, your gut microbiome begins to diversify, meaning it starts to contain many different types of microbial species. Higher microbiome diversity is considered good for your health. (7)

Interestingly, the food you eat affects the diversity of your gut bacteria.

Eating food

You are what you eat  (P4)

As your microbiome grows, it affects your body in a number of ways, including:

  • Digesting breast milk: Some of the bacteria that first begin to grow inside babies’ intestines are called Bifidobacteria. They digest the healthy sugars in breast milk that are important for growth. (8, 9, 10)

  • Digesting fiber: Certain bacteria digest fiber, producing short-chain fatty acids, which are important for gut health. Fiber may help prevent weight gain, diabetes, heart disease and the risk of cancer. (11, 12, 13, 14, 15, 16)

  • Helping control your immune system: The gut microbiome also controls how your immune system works. By communicating with immune cells, the gut microbiome can control how your body responds to infection. (17)

  • Helping control brain health: New research suggests that the gut microbiome may also affect the central nervous system, which controls brain function. (17)

Therefore, there are a number of different ways in which the gut microbiome can affect key bodily functions and influence your health. Find out more about how the microbiome affects your body in our series of articles here. 

Related Articles



  1. Sender, R., Fuchs, S. and Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, 14(8), p.e1002533.

  2. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Li, S., Jian, M., Zhou, Y., Li, Y., Zhang, X., Li, S., Qin, N., Yang, H., Wang, J., Brunak, S., Doré, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., Ehrlich, S. and Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), pp.59-65.

  3. The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease. (2014). Cell Host & Microbe, 16(3), pp.276-289.

  4. Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., Khan, M., Zhang, J., Li, J., Xiao, L., Al-Aama, J., Zhang, D., Lee, Y., Kotowska, D., Colding, C., Tremaroli, V., Yin, Y., Bergman, S., Xu, X., Madsen, L., Kristiansen, K., Dahlgren, J. and Wang, J. (2015). Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host & Microbe, 17(6), p.852.

  5. Hill, C., Lynch, D., Murphy, K., Ulaszewska, M., Jeffery, I., O’Shea, C., Watkins, C., Dempsey, E., Mattivi, F., Tuohy, K., Ross, R., Ryan, C., O’Toole, P. and Stanton, C. (2017). Erratum to: Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome, 5(1).

  6. Aagaard, K., Ma, J., Antony, K., Ganu, R., Petrosino, J. and Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Science Translational Medicine, 6(237), pp.237ra65-237ra65.

  7. Koenig, J., Spor, A., Scalfone, N., Fricker, A., Stombaugh, J., Knight, R., Angenent, L. and Ley, R. (2010). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences, 108(Supplement_1), pp.4578-4585.

  8. Arboleya, S., Watkins, C., Stanton, C. and Ross, R. (2016). Gut Bifidobacteria Populations in Human Health and Aging. Frontiers in Microbiology, 7.

  9. Turroni, F., Peano, C., Pass, D., Foroni, E., Severgnini, M., Claesson, M., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., Gueimonde, M., Margolles, A., De Bellis, G., O’Toole, P., van Sinderen, D., Marchesi, J. and Ventura, M. (2012). Diversity of Bifidobacteria within the Infant Gut Microbiota. PLoS ONE, 7(5), p.e36957.

  10. Turroni, F., Peano, C., Pass, D., Foroni, E., Severgnini, M., Claesson, M., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., Gueimonde, M., Margolles, A., De Bellis, G., O’Toole, P., van Sinderen, D., Marchesi, J. and Ventura, M. (2012). Diversity of Bifidobacteria within the Infant Gut Microbiota. PLoS ONE, 7(5), p.e36957.

  11. Marcobal, A. and Sonnenburg, J. (2012). Human milk oligosaccharide consumption by intestinal microbiota. Clinical Microbiology and Infection, 18, pp.12-15.

  12. Slavin, J. (2013). Fiber and Prebiotics: Mechanisms and Health Benefits. Nutrients, 5(4), pp.1417-1435.

  13. Sonnenburg, E., Smits, S., Tikhonov, M., Higginbottom, S., Wingreen, N. and Sonnenburg, J. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529(7585), pp.212-215.

  14. Ríos-Covián, D., Ruas-Madiedo, P., Margolles, A., Gueimonde, M., de los Reyes-Gavilán, C. and Salazar, N. (2016). Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health. Frontiers in Microbiology, 7.

  15. Dietary fibre and incidence of type 2 diabetes in eight European countries: the EPIC-InterAct Study and a meta-analysis of prospective studies. (2015). Diabetologia, 58(7), pp.1394-1408.

  16. Brown, L., Rosner, B., Willett, W. and Sacks, F. (1999). Cholesterol-lowering effects of dietary fiber: a meta-analysis. The American Journal of Clinical Nutrition, 69(1), pp.30-42.

  17. Rooks, M. and Garrett, W. (2016). Gut microbiota, metabolites and host immunity. Nature Reviews Immunology, 16(6), pp.341-352.


P1. Source Unknown

P2. Source Unknown

P3. Source Unknown


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