An Introduction to the Gut and Gut Microbiota

An Introduction to the Gut and Gut Microbiota

The trillions of microorganisms and their genetic material that live in your intestinal tract comprise your 'gut microbiome.' These microorganisms, primarily bacteria, perform vital functions for your health and well-being.

An Introduction to the Gut and Gut Microbiome


Ever looked at a menu and noticed that you have got a watery mouth or that your stomach is churning? And do you know who’s behind the scenes? That’s what we’ll be talking about here!

It’s time to meet your GUT!!

What is the gut? How is it linked to the human body? Well, calm down! Although there has been a recent explosive increase in the number of articles written on the gut, we’ve got you covered with the real definition.

on and role of the human gut in our lives! So, let's delve into the world of microbes in your body.

What is the Gut?

Technically, the gut is the digestive system or gastrointestinal tract (GI) - a pathway from your mouth to your rear. It is a complex ecosystem inhabited by a myriad of microorganisms, including fungi, bacteria, viruses, and archaea. This ecosystem, collectively known as the ‘microbiota’, provides various protective, structural, and metabolic benefits to the human body (1, 2).


“About 100 trillion bacteria reside in the gut and produce numerous health effects (3).”

The development of the GI tract in early life

Our GI system is subject to significant structural changes from birth into the early years of life. Experts have marked the following changes to the GI tract (4-5):

  • At birth, the stomach of an infant is the size of a cherry and can hold just 5-7 ml of milk
  • By day three, the infant’s stomach is the size of a walnut and can hold around 22-27 ml of fluid.
  • By the end of the first month, the stomach can hold between 80 and 150 ml and is around the size of an egg.
  • The small intestine undergoes dramatic change - it almost doubles in length from 275 cm at birth to over 450 cm by the age of five years.

Similarly, the gut goes through a remarkable period of physiological growth. The development of the human gut is an interdependent process that includes the formation of the digestive system. Additionally, some of the vital biochemical and neurological processes develop over the first year after birth. Therefore, the healthy development of our GI tract is directly linked to our overall health and well-being.

Functions of the Gut

The primary functions of the gut are digestion, absorption of essential nutrients, and the excretion of waste products (6). Therefore, it has a major influence on both the development and function of the immune system. Apart from this, some of the significant functions of the gut are (7-9):

  • Vitamin synthesis
  • safeguards against pathogens
  • increased fat storage efficiency
  • Central nervous system (CNS) modulation

and many more…..

Now that we've covered the fundamentals of the gut, let's take a quick look at the gut microbiome and its role in health.

What is the Gut Microbiome?

Imagine a rainforest with thousands of different species. All of these have their own niche in the forest. The same thing happens in your gut. On a microscopic scale, thousands of microbial species form a complex network to cooperate, compete, and fight for their niche.

We have well over a trillion little microbes present in and around our bodies, mostly in our large intestines. This complex habitat of microorganisms, their genes, and the surrounding environmental conditions is called the gut microbiome or microbiota (10).

The human gut microbiome comprises the collective genomes of microorganisms inhabiting us, namely bacteria, archaea, protozoa, eukaryotes, and viruses that live symbiotically within various sites of our body. Some of the significant occupied habitats include the oral cavity, respiratory tract, skin, gastrointestinal system, and genital organs(11).

Each individual has a unique set of microorganisms, called microbiota. The most abundant microbiota are found in the gut, specifically the human colon, an organ that supports the most microbes. The four dominant phyla resident in the human gut are:

  • Firmicutes,
  • Bacteroidetes
  • Actinobacteria
  • Proteobacteria

Most bacteria belong to the genera Bacteroides, Bifidobacterium, Clostridium, Eubacterium, Fusobacterium, Peptococcus, Peptostreptococcus, and Ruminococcus. Other genera, such as Escherichia and Lactobacillus are present to a much lesser extent. Species from the genus Bacteroides are important in the functioning of your body since they alone constitute about 30% of all bacteria in the human gut (12).

Your GUT Microbiome and General Health

The gut microbiome influences the body from birth across the entire lifespan, by controlling food digestion, the immune system, the central nervous system, and other bodily processes (13-15). It also influences blood sugar control and may influence the onset of type 1 diabetes in children (16, 17). By producing brain chemicals and communicating with nerves that connect to the brain, the gut microbiome may influence brain health (18, 19).

It's about time you started paying attention to your gut health and started living a healthier life. Optimal gut health is the balanced functioning of bacteria in many parts of the GI tract.

As discussed earlier, the gut microbiome helps you with a wide range of bodily functions as it is directly linked to many organs in your body. Hence, make sure the journey towards a healthier gut does not involve - bad diets, stress, sleep issues, vitamin deficiencies, gut-disrupting medicines, and infections that result in poor gut health.

We shall learn more about the direct links between the gut and other essential organs of the body in our upcoming blog pieces. Till then, Stay Gut Healthy!


  1. S. Ahlawat, Asha,K.K. Sharma. Gut–organ axis: a microbial outreach and networking, 29 May 2020
  2. de Steenhuijsen Piters WA, Sanders EA, Bogaert D. The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond B Biol Sci. 2015 Aug 19;370(1675):20140294. doi:10.1098/rstb.2014.0294. PMID: 26150660; PMCID: PMC4528492.
  3. Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project. Nature 449, 804–810 (2007).
  4. Bilgen H, Kültürsay N, Türkyılmaz C. Turkish Neonatal Society guideline on nutrition of the healthy term newborn. Turk Pediatri Ars. 2018 Dec 25;53(Suppl 1):S128-S137. doi: 10.5152/TurkPediatriArs.2018.01813. PMID: 31236026; PMCID: PMC6568295.
  5. Weaver LT, Austin S, Cole TJ. Small intestinal length: a factor essential for gut adaptation. Gut. 1991 Nov;32(11):1321-3. doi: 10.1136/gut.32.11.1321. PMID: 1752463; PMCID: PMC1379160.
  6. Hornbuckle WE, Simpson KW, Tennant BC. Gastrointestinal Function. Clinical Biochemistry of Domestic Animals. 2008:413–57. doi: 10.1016/B978-0-12-370491-7.00014-3. Epub 2008 Oct 22. PMCID: PMC7173558.
  7. Gail A. Cresci, PhD, RD, LD, CNSC, Associate Staff and Emmy Bawden, RD. The Gut Microbiome: What we do and don’t know, 2015 Oct 8. doi: 10.1177/0884533615609899
  8. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15718-23. doi: 10.1073/pnas.0407076101. Epub 2004 Oct 25. PMID: 15505215; PMCID: PMC524219.
  9. Ma, Q., Xing, C., Long, W. et al. Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis. J Neuroinflammation 16, 53 (2019).
  10. Berg, Gabriele et al. “Microbiome definition re-visited: old concepts and new challenges.” Microbiome vol. 8,1 103. 30 Jun. 2020, doi:10.1186/s40168-020-00875-0
  11. Dekaboruah, Elakshi et al. “Human microbiome: an academic update on human body site specific surveillance and its possible role.” Archives of microbiology vol. 202,8 (2020): 2147-2167. doi:10.1007/s00203-020-01931-x
  12. Linares, Daniel M et al. “Beneficial Microbes: The pharmacy in the gut.” Bioengineered vol. 7,1 (2016): 11-20. doi:10.1080/21655979.2015.1126015
  13. Oliphant, K., Allen-Vercoe, E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome 7, 91 (2019).
  14. Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016 May 27;16(6):341-52. doi: 10.1038/nri.2016.42. PMID: 27231050; PMCID: PMC5541232.
  15. Cryan, John F, and Timothy G Dinan. “Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour.” Nature reviews. Neuroscience vol. 13,10 (2012): 701-12. doi:10.1038/nrn3346
  16. Kostic, Aleksandar D et al. “The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.” Cell host & microbe vol. 17,2 (2015): 260-73. doi:10.1016/j.chom.2015.01.001
  17. Zeevi, David et al. “Personalized Nutrition by Prediction of Glycemic Responses.” Cell vol. 163,5 (2015): 1079-1094. doi:10.1016/j.cell.2015.11.001
  18. O'Mahony, S M et al. “Serotonin, tryptophan metabolism and the brain-gut-microbiome axis.” Behavioural brain research vol. 277 (2015): 32-48. doi:10.1016/j.bbr.2014.07.027
  19. Forsythe, Paul et al. “Vagal pathways for microbiome-brain-gut axis communication.” Advances in experimental medicine and biology vol. 817 (2014): 115-33. doi:10.1007/978-1-4939-0897-4_5
  20. Patterson, Elaine et al. “Gut microbiota, obesity and diabetes.” Postgraduate medical journal vol. 92,1087 (2016): 286-300. doi:10.1136/postgradmedj-2015-133285


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