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How Does Microbiome Affect Immune System

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The Crosstalk Between The Gut And The Immune System

Linking the Gut Microbiome, Obesity, and the Immune System

The immune system is the group of cells and molecules that protect us from disease by monitoring our body and responding to any foreign substances they perceive as threats, particularly infectious microbes. Our immune system has co-evolved along with a diverse gut flora, not only to create defenses against pathogens, but also to develop tolerance for beneficial microbes. As a consequence, the immune system and the gut microbiota developed a mutualistic relationship, regulating one another and cooperating to support each other. The importance of this interaction is clearly highlighted by the fact that 7080% of the bodys immune cells are found in the gut.

The dialogue between the immune system and the microbiota starts the moment our body gets in contact with microbesat birth. As we grow, the microbiota shapes the development of our immune system, and the immune system shapes the composition of the microbiota. This communication and mutual regulation is maintained throughout life and is the key for a healthy interaction between the microbiota and the immune system.;

Our immune system co-evolved with the gut microbiota. Both work together to keep us healthy and protect us against unwanted microbes.

Microbiome Medicine: Scientists Harness The Bodys Bugs To Treat Asthma Ms And More

Plenty of probiotic yogurts, pickles;and kombuchas claim to boost our digestive health with armies of microbes, but some scientists have more ambitious therapeutic plans for the bugs that colonize us. They hope to leverage these microbes as living therapeutics;for a range of health conditions, including ulcerative colitis, multiple sclerosis, eczema, and asthma.;

It Affects Gut Health

The microbiome can also affect gut health and may play a role in intestinal diseases like irritable bowel syndrome and inflammatory bowel disease (


A healthy gut microbiome controls gut health by communicating with the intestinal cells, digesting certain foods and preventing disease-causing bacteria from sticking to the intestinal walls.

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Why Immunoglobin A Is Important For Gut Immunity

One of the most important molecules involved in the crosstalk between the immune system and the microbiota is immunoglobulin A . IgA is a type of antibody produced by specific B cells known as plasma cells. IgA can bind and coat specific microbes, microbial components, dietary components, and other antigens in the intestine. This creates an additional physical barrier that prevents potentially harmful interactions with the immune system.;

IgA supports the establishment of a balanced microbiota by regulating its composition, controlling microbial gene expression, increasing microbial diversity, and enhancing mutualism between the gut microbiota and the host. In turn, the gut microbiota affects the production of IgA by influencing the accumulation of plasma cells, as well as the diversity and magnitude of IgA responses. The IgA repertoire in the gut is constantly adjusted in response to changes in microbial composition, with increases in microbial diversity leading to increases in the diversity of the IgA pool.

In the crosstalk between the gut microbiota and the immune system, there is another type of cell that plays a significant part: TH17 cells, a type of helper T cell. TH17 cells located in the intestinal wall stimulate the production of antimicrobial proteins, including IgA, and enhance the integrity of the intestinal mucosal barrier, thereby having a beneficial role in preventing infection and promoting homeostasis.;

How Microbiota Benefit The Body

Immune system vs. gut bacteria: How vitamin A

Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.

Sugars like table sugar and lactose are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohns disease, and antibiotic-associated diarrhea.

The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.

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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 .

Whats 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 .

Altogether, these microbes may weigh as much as 25 pounds , 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.


The gut microbiome refers to all of the microbes in your intestines, which act as another organ thats crucial for your health.

Keeping Your Microbiome In Good Shape

As far we know the best way to establish and maintain a healthy gut microbiome is to get enough sleep and exercise, eat healthy meals that include lots of fruits and vegetables, avoid chronic and excessive stress and not to drink too much. You can also help maintain healthy gut bacteria by taking antibiotics only when they are necessary. Remember, antibiotics dont help if you have a virus, such as colds or the flu.

By Elizabeth Bent, Research Associate at University of Guelph. Bent receives funding from the Ontario Ministry of Agriculture and Food, and the Natural Sciences and Engineering Research Council of Canada. She consults to her own company, Renaissance Biological Solutions, Inc. She does not work with or research vaccines, though she does work with different kinds of microbiomes, and bacteria isolated from microbiomes. This article was originally published on The Conversation. Read the original article.

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Unhealthy Gut Bacteria Can Make Vaccines Less Effective

Scientists have started examining the interactions between gut bacteria and responses to vaccines. A recent review article concluded that the composition of your gut microbiome can influence whether a vaccine has an effect in your body.

Unhealthy gut microbiome composition can lead to inflammation. And that means more bacterial cells pass through the damaged lining of the gut, which stimulates further immune system responses. This is called leaky gut. Vaccines may not be as effective because the immune system is already busy dealing with these bacterial cells leaking through the gut.

On the other hand, having a diverse and healthy gut microbiome, and thus no gut inflammation and leakiness, might allow a persons immune system to focus on responding to the vaccine effectively.

Recent research has also found that the effectiveness of the seasonal flu shot could be enhanced by intestinal bacteria. The immune system detects specific proteins from the bacteria, and this detection seems to increase the immune systems response to the flu vaccine. Then your body has an easier time mounting an immune response if you are exposed to the real flu virus.

Could an unhealthy gut microbiome be the culprit in the rare cases when a person has an unexpected immune reaction to a vaccine, such as an anaphylactic reaction? We dont know for certain yet, but it is a possibility.

Role Of The Microbiota In Cancer

The Gut Microbiome’s Impact on The Immune System

Perhaps the first indication that the commensal microbiota could drive cancer was provided by the observation that stomach ulcers and subsequent stomach cancer were caused by the presence of a single type of bacteria Helicobacter pylori . The vast majority of people carrying H. pylori are asymptomatic and thus as for most host-microbe interactions, the host response to the colonization determines whether chronic inflammation and carcinogenesis occurs. Similar phenomena seem to be important to the etiology of cancers at other barrier surfaces, most notably the intestine. On the other hand, H. pylori is associated with protection from other types of cancer further highlighting the functional contextuality of commensal.

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Why Plant Fibers Are Critical For Brain And Immune Health

Gut microbes get most of their nutrients from our diet and help us digest much of the food we ingest. Therefore, it should come as no surprise that diet has a huge impact on the composition of gut microbiota and, consequently, on our immune system. Diet influences many aspects of the microbiota-immune system crosstalk, including, for example, the permeability of the intestinal barrier, the types of microbes targeted by IgA, or whether TH17 cells become beneficial or harmful.;

Modern diets, particularly those of the Western world, are characterized by an excessive intake of highly palatable energy-dense foods, including high levels of animal protein, saturated fats, simple sugars, and salt, but low amounts of plant-derived fibers. And this is exactly the dietary pattern that is being increasingly linked to immune dysfunctions associated with the gut microbiota. For example, high dietary intake of salt or of long-chain and saturated fatty acids may stimulate the harmful actions of TH17 cells, which, in turn, may increase the risk of autoimmune reactions.;

SCFA, like acetate and butyrate, are made when gut microbes ferment insoluble fiber and carbohydrates . Eating a diet rich in plant foods that can be converted into SCFA helps keep the brain and immune system healthy.

The Dysbiosis Of The Gut Microbiome Induces Intestinal Diseases

Altered microbiota diversity was found in IBD, and it was reflected by a decline in commensal bacteria, such as Firmicutes and Bacteroidetes, and an increase in detrimental bacteria, such as Proteobacteria and Actinobacteria . Due to the decreased microbial diversity in IBD, the ability of microbiota to adapt to environmental changes and to defend against natural disturbances is impaired. Active bacterial products can regulate the inflammatory response in IBD. For example, IL-10 deficiency was found to be associated with early-onset IBD . SCFAs are dietary fiber produced by gut bacteria fermentation. Studies of fecal samples from IBD patients showed that SCFA levels were remarkably changed, supporting the important role of SCFAs in IBD . SCFAs regulate certain inflammatory responses by binding GPR43 . Additionally, SCFAs regulate colonic Treg cell homeostasis by restoring the colonic size and function of the Treg cell pool in GF mice .

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Interactions Between The Adaptive Immune System And The Microbiota

Follicular helper T cells are specialized to assist B cells, and are crucial for germinal center formation, affinity maturation, and generation of high-affinity antibody responses and memory B cells. Tfh cells are implicated in maintenance of microbiota homeostasis as highlighted by studies showing that impairment of Tfh cells resulting from lack of expression of co-receptor programmed cell death 1 or ATP-gated ionotropic P2RX7 receptor can alter gut microbiota composition., The relationship between Tfh cells and the microbiota is reciprocal, as Tfh cell differentiation is impaired in GF mice and can be restored by administration of Toll-like receptor 2 agonists that activate T cell-intrinsic MyD88 signaling. In mice, SFB can induce Tfh cell differentiation in Peyers patches by limiting the access of IL-2 to CD4+ T cells, thereby amplifying the master regulator Bcl-6 of Tfh cells. The microbiota-Tfh axis may also be relevant in autoimmune diseases, as in mice SFB-induced Tfh cell differentiation can boost autoantibody production and thus exacerbate arthritis.

How Can Bacteria In Your Gut Interact With Your Immune System

Immune system vs. gut bacteria: How vitamin A

We are still learning how gut bacteria and the immune system interact. Research suggests that the interaction evolved over time to manage the balance between reacting to harmful pathogens and tolerating non-harmful organisms. You want your immune system to react to the pathogens that can make you sick, while letting the beneficial bacteria living in your gut go about their business.

We are still learning what a healthy gut microbiome looks like. Evidence suggests that a balanced and diverse microbiome might contribute to better health overall, and a less diverse or less balanced microbiome can have a negative impact on health.

A review article from 2014 suggests that the overuse of antibiotics, changes in diets and the elimination of beneficial organisms that work with bacteria in high income countries may have resulted in gut microbiomes that lack the resilience and diversity of functions required to establish balanced immune responses. Why does that matter?

Having less diverse gut bacteria has been linked to inflammatory bowel diseases and the increase in autoimmune diseases in developed countries.

For instance, a 2013 study found that children living in Bangladesh have more diverse gut microbiomes than children from the United States. Researchers suggest that dietary differences with children in the US eating more animal fats and protein are a factor.

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What Is Our Immune System

On a daily basis, we are constantly exposed to potentially harmful microbes of all sorts. Our immune system, a network of intricate stages and pathways in the body, protects us against these harmful microbes as well as certain diseases. It recognizes foreign invaders like bacteria, viruses, and parasites and takes immediate action. Humans possess two types of immunity: innate and adaptive.

Innate immunity is a first-line defense from pathogens that try to enter our bodies, achieved through protective barriers. These barriers include:

  • Skin that keeps out the majority of pathogens
  • Mucus that traps pathogens
  • Stomach acid that destroys pathogens
  • Enzymes in our sweat and tears that help create anti-bacterial compounds
  • Immune system cells that attack all foreign cells entering the body

Adaptive or acquired immunity is a system that learns to recognize a pathogen. It is regulated by cells and organs in our body like the spleen, thymus, bone marrow, and lymph nodes. When a foreign substance enters the body, these cells and organs create antibodies and lead to multiplication of immune cells that are specific to that harmful substance and attack and destroy it. Our immune system then adapts by remembering the foreign substance so that if it enters again, these antibodies and cells are even more efficient and quick to destroy it.

Other conditions that trigger an immune response

What factors can depress our immune system?

Gut Microbiome Regulates The Intestinal Immune System

Brown University
A new study in mice unveils the role of vitamin A in immune system regulation, a finding that could assist in developing treatments for autoimmune and inflammatory diseases as well as vitamin A deficiency.

Scientist have long known that bacteria in the intestines, also known as the microbiome, perform a variety of useful functions for their hosts, such as breaking down dietary fiber in the digestive process and making vitamins K and B7.

Yet a new study unveils another useful role the microbiome plays. A team of researchers from Brown University found that in mice, the gut microbiome regulates the host’s immune system — so that rather than the host’s defense system attacking these helpful bacteria, the bacteria can co-exist peacefully with the immune system.

What’s the trick to the microbiome’s work with the immune system? Vitamin A — the bacteria moderate active vitamin A levels in the intestine, protecting the microbiome from an overactive immune response.

That insight may prove important for understanding and treating autoimmune and inflammatory diseases, said Shipra Vaishnava, an assistant professor of molecular microbiology and immunology at Brown.

The study was published on Tuesday, Dec. 18, in the journal Immunity.

Microbiomes of mice and men

Vaishnava expects the findings are generalizable to the interactions between the human microbiome and their hosts as well.

Helping human health

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Myth: Antibiotics Do Not Harm The Immune System

Fact: Although antibiotics do not directly interfere with the immune system, unnecessary antibiotic usage can stop the immune system from working to its full potential. In fact, antibiotics can also compromise the immune system of the body.

A research study conducted on mice found that when antibiotics were injected into the mice, the cells’ biochemical environment changed. Often the antibiotic exposure reduces the ability of the macrophage cells to engulf the bacteria.

Why It Is Worth Taking The Gut Microbiota Into Account In The Fight Against Covid

Close Friends: The Microbiome and the Immune System

The idea that bodily organs and tissues opened to the outside are connected is not new. For instance, the lungs and gut microbiota influence each other and that relationship may keep your lungs healthy.

In this case, scientists have reported the presence of SARS-CoV-2 in the stool samples of people who have the virus. Furthermore, some COVID-19 patients showed an altered gut microbiota composition with decreased beneficial bacteria, which included Lactobacillus and Bifidobacterium.

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Food To Restore Gut Bacteria

Certain food can help restore the gut bacteria, especially after undergoing a long course of antibiotics. Fermented food like curd, kimchi, cheese, and kombucha are loaded with good bacteria like Lactobacilli and Bifidobacteria, which helps restore balance in the gut.

Eating fiber-rich food also helps the gut bacteria to restore balance. While on antibiotics, you should eat high fiber food like bananas, lentils, nuts, whole grains, beans, broccoli, peas, berries, etc.

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