Our body, in particular our gastrointestinal tract, is host to billions of microbes. Some of them such as Bifidobacterium are beneficial, preventing gut inflammation, whilst others like Staphylococcus aureus are notorious for potentially leading to fatal diseases such as sepsis.
Sepsis- the body’s overwhelming and life-threatening response to infection that can lead to tissue damage, organ failure, and death. In other words, it’s your body’s overactive and toxic response to an infection.
Our immune system must be able to differentiate between the favourable and the threatening– and this response is mediated by T cells.
What are T cells?
T cells are a type of immunity related cell produced in the thymus with around 50000000 formed every day. Yet only around 2-4% of these leave thy thymus alive and mature. Why is this? Because of a process called T cell education.
thymus- an organ located behind the breastbone playing an important part in immunity and hormonal regulation
What is T cell education?
A selection process ensuring that T cells can differentiate your own cells from foreign cells. There are 2 steps to this process:
The first kills off the T cells which don’t recognise your own Major Histocompatibility complex at all.
Major Histocompatibility complex- Molecule monitoring the surface of your own cells
The second step eliminates those cells which are too attracted to your own Major Histocampatibility complex. 
This process occurs in the thymus and protects your own cells. But what about protecting bacteria? They may live in you, but are their own separate cells.
T cell education- but in the gut!
In the gut a similar process occurs. Cells called innate lymphoid cells educate T cells and are able to form a physical barrier between immune system cells and beneficial bacteria, thereby protecting them.
The importance of innate lymphoid cells have been also studied in gut disorders such as Crohn’s disease.
Crohn’s disease- chronic inflammation of the lining of the digestive system.
In one study individuals with this disease had Innate lymphoid cells lacking specific molecules responsible for the education of T cells.  Therefore T cells could attack the gut as well as its bacteria causing inflammation.
Overall a healthy immune system plays a large role it protecting not only our own cells and own health, but also our microbial residents.
 Healthline. (2016). 10 Ways to Improve Your Gut Bacteria, Based on Science. [online] Available at: https://www.healthline.com/nutrition/improve-gut-bacteria#section2 [Accessed 12 Jul. 2019].
 NIH. (2018). Probiotic bacteria block harmful microbe. Available at: https://www.nih.gov/news-events/nih-research-matters/probiotic-bacteria-block-harmful-microbe [Accessed 12 Jul. 2019].
 Sepsis Alliance. (n.d.). Definition of Sepsis. [online] Available at: https://www.sepsis.org/sepsis-basics/what-is-sepsis/ [Accessed 12 Jul. 2019].
 InterPro. (2019). Major Histocompatibility Complex. [online] Available at: https://www.ebi.ac.uk/interpro/potm/2005_2/Page1.htm [Accessed 12 Jul. 2019].
 American Microbiome Institute. (2015). Immune system cells are educated in the gut to not attack beneficial gut bacteria. Available at: http://www.microbiomeinstitute.org/blog/2015/4/28/immune-cells-are-educated-in-the-gut-to-not-attack-beneficial-bacteria [Accessed 12 Jul. 2019].