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The Gut Microbiome and The Immune System: Allies or Not?

✍🏼 Sameeha Jaffer Ali | BSc Biomedical Science Graduate from Aston University


What is the gut microbiome? 🦠

The gut microbiome or microbiota is the diverse community of microbes – including bacteria, fungi, viruses and protozoa – that reside in the gut.

The gut microbiome has many health benefits. However, when microbe populations become imbalanced (also known as dysbiosis), the gut microbiome can be problematic. A staggering number of approximately 100 trillion microbes are thought to inhabit your digestive system, outweighing the number of human cells present.

The gut microbiome assists your body in many roles, including:

  • Digestion

  • Absorption

  • Control of the chemical reactions in cells (metabolic regulation)

  • Structural maintenance of the intestines

  • Defence against disease

The composition of your gut microbiome develops from birth and is unique to everyone. As you move into adulthood, the composition becomes more diverse and is influenced by factors such as your diet, exercise, and antibiotic use.


What is the immune system? ⚔️

The immune system is the biological system that protects and defends your body against disease.

The main role of your immune system is to fight off and facilitate any damage repair resulting from disease-causing organisms, known as pathogens. Pathogens can be anything from bacteria, viruses, fungi and parasites.

Your immune system cleverly fends off pathogens using three lines of defence:

1st Line: Physical and Chemical Barriers

The first line of defence comprises of structures like your skin and mucous membranes (moist tissue lining that produce mucus) that act as physical barriers to trap and prevent pathogens from reaching important internal organs.

Your body's fluids such as saliva, sweat and tears, act as chemical barriers that break down pathogens using the proteins within them.

2nd Line: Innate Response

The second line of defence is general response used for any pathogen that has successfully invaded your system.

Here, your white blood cells rush to the site of infection and destroy pathogens by engulfing and breaking them down. Pathogens possess a structural subpart called an antigen, which the immune system uses to identify and attack foreign matter.

3rd Line: Adaptive Response

The last line of defence is a highly specific response that targets pathogens the body has already previously encountered. Your immune system keeps a record of pathogens that it has met before, enabling it to mount a faster and more precise response the second time it meets them.

Here, your white blood cells produce proteins that bind specifically to antigens, called antibodies, These inactivate pathogens and render them harmless.


How does the immune system affect the gut microbiome?🧫

The immune system ensures the gut microbiome is under control.

A healthy immune system acts as a shield, defending against foreign invaders and maintaining your microbiome, without attacking your own cells.

If your immune system is weakened, it loses its ability to maintain a healthy composition of microbial communities in your gut. This can lead to an overgrowth of harmful bacteria and make you vulnerable to infection. Moreover, some harmless bacteria that usually live peacefully in your gut can become hostile and infect you when your immune system is compromised and defenceless - a vivid example of 'good guys turned bad'.


How does the gut microbiome affect the immune system?💪🏻

The gut microbiome encourages the training and development of immune cells.

Studies conducted on germ-free mice have revealed that certain bacterial strains within your gut promote the development of white blood cells that are involved in both the innate and adaptive immune response. Some have also been shown to encourage the training and education of cells that produce antibodies (plasma cells), resulting in increased antibody production and an enhanced immune response.


How is the gut microbiome linked to autoimmunity? 🤒

An imbalanced gut microbiome can promote inflammation in autoimmune diseases.

Autoimmunity occurs when the immune system becomes overactive and mistakenly attacks healthy cells and tissue. One in ten individuals are thought to be affected by autoimmune diseases. Examples of common autoimmune diseases include:

· Inflammatory Bowel Disease

· Lupus

· Multiple Sclerosis

· Rheumatoid Arthritis

The exact cause of autoimmune diseases remain unknown, but those who are genetically predisposed and exposed to environmental triggers, like gut dysbiosis, have higher risk of developing an autoimmune disease.

An imbalanced gut not only loses its immune-boosting effects but also promotes inflammation (characterised by pain, redness, heat, and swelling) in autoimmune patients. When disturbed, specific bacterial species in the gut can trigger the release of components that tell your body to begin an inflammatory response (called pro-inflammatory cells), destroying healthy cells and driving further damage.


Why is research in this field important?🔬

Studying the gut microbiome-immune system link can help us create new treatments for autoimmune diseases.

Current research demonstrates your gut microbiome and immune system maintaining a harmonious relationship for the most part, with your immune system regulating your gut microbiome and your gut microbiome strengthening your immune responses. However, disturbances to the gut microbiome can negatively impact your immunity and accelerate the destruction of healthy cells and tissues in an autoimmune condition.

While scientific research has continuously acknowledged the importance of maintaining a healthy gut microbiome for enhanced digestive health and immunity, the journey of discovery should not end here. By further investigating the gut microbiome, we can better understand its role in autoimmune diseases and pave the way for new therapies that focus on restoring the ideal balance of microbes in the gut.

The editor of the piece, on a lilac background

Edited by: Olivia Laughton | Content Editor | BSc Microbiology, University of Leeds


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aijaz ali khushik
aijaz ali khushik
Nov 18, 2023

The gut microbiome and the immune system have a complex and interconnected relationship. While they can act as allies in maintaining health, there are also instances where their interactions can lead to dysregulation and contribute to certain diseases. Here's a closer look at their relationship:

1. Allies: The gut microbiome and the immune system can work together to promote overall health and immune function. The gut microbiome, which consists of trillions of microorganisms residing in the gastrointestinal tract, helps train and educate the immune system. It plays a crucial role in the development and maturation of immune cells and helps maintain a balanced immune response. The microbiome also helps regulate the integrity of the gut barrier, preventing the entry of…


aijaz ali khushik
aijaz ali khushik
Nov 18, 2023

The gut microbiome and the immune system have a complex relationship, and they can be considered both allies and adversaries depending on the circumstances. Let's explore this connection further.

The gut microbiome refers to the trillions of microorganisms, including bacteria, viruses, fungi, and other microbes, that reside in the gastrointestinal tract. These microbes play a crucial role in maintaining our overall health, including our immune system.

In terms of allies, the gut microbiome and the immune system work together in several ways:

1. Immune Development: The gut microbiome helps in the development and maturation of the immune system, especially in early life. It stimulates the production of immune cells and helps establish a balanced immune response.

2. Barrier Function: The…


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