A Marvellous Microbiome


Our existence is a result of cells working together. Red blood cells transport O2 around the body. Sensory neurones send electrical impulses to the Central Nervous System. But, not all cells in our body are human cells as they are not coded by our DNA. An average man, defined as 70 kilograms, 20–30 years old and 1.7 metres tall, has around 30 trillion human cells, and 39 trillion bacteria cells. Over 50% of the human body isn’t ‘human’!

Though other microorganisms, such as viruses and fungi, are present, they are vastly outnumbered by bacteria. But where are they found? The most well-known hub of bacteria lies in the gut, also known as the gastrointestinal tract. Other locations of micro-biomes in the body include the eyes, mouth, skin and lungs, but there are many more anatomical regions where the flora reside.

As bacteria aren’t human cells, the antigens on their surface are foreign. You would expect the immune system to launch an attack against them, but the significant number of flora (bacterial life) tell a different story. Yes, there are ‘bad’ bacteria in the GI tract that are dealt with, but there are also ‘good’ bacteria. The issue that arises if an immune response occurs, is that there is a risk of damage caused by inflammation. In the gut, Innate Lymphoid Cells (ILCs) prevent T-cells from destroying the flora. ILCs are often found in the lamina propria, a thin layer of connective tissue in the mucosa of the GI tract. They cause maturation of some T-cells into mature regulatory cells, which prevent the inflammation, and ILCs also destroy T-cells that are attacking gut flora.

So how can bacteria be ‘good’, as mentioned previously? First, let’s look at the gut flora. Some bacteria are very efficient at synthesising Vitamin K, which enters the blood via lacteals in the small intestines. Different Lactic Acid Bacteria can synthesise different vitamins. Apart from vitamin synthesis, some bacteria are also able to digest cellulose, something we can’t digest by ourselves, increasing nutrient absorption efficiency. Bacteria can even break down fibres into short-chain fatty acids, which are easily absorbed in the lacteals. There are many other roles that bacteria play in the GI tract, showing how useful and important they are.

Another benefit of the microbiome is that it can train the immune system. An example of this can be found in the eye. For a while, it was thought that the eye was sterile due to the secretion of lysozymes. However, studies on mice showed that there is indeed a micro-biome present . The bacteria here can secrete interleukins. Interleukins are glycoproteins that are vital for triggering an immune response. This attracts neutrophils, an abundant type of white blood cell, that can repair any damage and help fend off pathogens. Gut bacteria are essential in training our immune systems from the day that we are born. As babies, our immune systems aren’t efficient, but rapidly improve, with gut flora helping out. It turns out that the way we are born can significantly affect the type of gut flora. Those born via C-section have a relatively higher risk of type-1 diabetes and asthma, perhaps due to an increased exposure to bacteria and the weak immune system. Another example can be found on the skin. Our skin is exposed to countless microorganisms, and some of them may enter the body. This can educate the billions of T-cells near the skin, improving the immune response if a pathogen breaches this barrier. Throughout the body and the skin, some viruses can be useful when dealing with bacteria. Known as bacteriophages, or phages, these viruses are adapted to infecting bacteria, multiplying in them and killing them.

It’s clear that our microbiome is a very important part of us, so how can it be compromised, and what are the consequences? One threat to our micro-biome is antibiotics. Unlike our immune system, antibiotics don’t discriminate in the bacteria they affect. If treated with antibiotics at a young age, the risk of asthma is higher. But in older people, much of the ‘lost’ bacteria is replenished, so the impact isn’t too serious. However, the benefit of antibiotics taken appropriately, outweigh these risks because they are getting rid of life-threatening diseases. As discussed previously, the type of birth can have impacts on the micro-biome present, but over time, the deficiencies caused by C-section should disappear. If T-cells in the gut aren’t functioning correctly and start attacking the bacteria, an immune response will be initiated, creating inflammation. While inflammation is a normal immune response, it can sometimes cause damage in the intestines. This can cause diseases such as Crohn’s disease and ulcerative colitis. But how can this occur? Studies on patients with Crohn’s disease showed that the ILCs lacked certain Major Histocompatibility Complex (MHC) Class II molecules. These molecules present antigens, which in this case, is essential to train the T-cells not to attack bacteria with these specific markers. Perhaps, a therapy that restores these MHC molecules could be used to treat these diseases.

Overall, our micro-biomes are fascinating parts of our bodies that contribute to our overall physical health. The more diverse our flora is, the healthier we are. Thus, something as simple as eating a balanced and varied diet can be hugely beneficial to us!


  1. McKeon, D. and McKeon, D., 2015. Immune Cells Are Educated In The Gut To Not Attack Beneficial Bacteria — The American Microbiome Institute. [online] The American Microbiome Institute. Available at: <http://www.microbiomeinstitute.org/blog/2015/4/28/immune-cells-are-educated-in-the-gut-to-not-attack-beneficial-bacteria> [Accessed 24 May 2020].
  2. Sciencedirect.com. n.d. Gut Flora – An Overview | Sciencedirect Topics. [online] Available at: <https://www.sciencedirect.com/topics/immunology-and-microbiology/gut-flora> [Accessed 24 May 2020].
  3. Han, L., Wang, X., Di, S., Gao, Z., Li, Q., Wu, H., Wang, Q., Zhao, L. and Tong, X., 2019. Innate Lymphoid Cells: A Link between the Nervous System and Microbiota in Intestinal Networks. Mediators of Inflammation, 2019, pp.1-11.
  4. Abbott, A., 2016. Scientists bust myth that our bodies have more bacteria than human cells. Nature,.
  5. ScienceDaily. n.d. Eye Microbiome Trains Immune Cells To Fend Off Pathogens In Mice. [online] Available at: <https://www.sciencedaily.com/releases/2017/07/170711125700.htm> [Accessed 24 May 2020].
  6. Medicalxpress.com. 2018. Why Gut Bacteria Are Essential For A Healthy Immune System. [online] Available at: <https://medicalxpress.com/news/2018-03-gut-bacteria-essential-healthy-immune.html> [Accessed 24 May 2020].
  7. Grice, E. and Segre, J., 2011. The skin microbiome. Nature Reviews Microbiology, 9(4), pp.244-253.
  8. Callaway, E., 2019. C-section babies are missing key microbes. Nature,.


Leave a Comment