BiotiQuest® Gut Health & Probiotics Blog with Martha Carlin

Understanding Gut Immunity — Probiotics and the Immune System

Martha Carlin | Mar 28, 2024 | 9 minute read

Your gut houses up to 70% of the immune system as it deals with an ever-changing passage of foreign substances, including food and pathogens. The gut microbiome plays an irreplaceable role in the development, maturation, and maintenance of the different layers of gut immunity. 

Probiotics and the immune system work hand in hand to support gut health and robust immunity. Your gastrointestinal tract is teeming with trillions of microorganisms, collectively known as the gut microbiota, helping you digest food, produce vitamins, develop and mature immune cells, and train your immune system.

To understand the different ways probiotic bacteria might affect immune health, let us dive into factors that contribute to the probiotic effects on gut health and the immune system.

Gut microbiome and gut health

Your gut flora contains a mix of specific beneficial bacteria. Beneficial bacteria consume complex carbohydrates such as fiber and resistant starches to produce metabolites that have several beneficial effects on your health. However, even helpful microorganisms can become pathogenic in an unhealthy gut environment.

Out of the most studied bacterial metabolites that support gut health and immune function are organic acids like lactic acid and short-chain fatty acids (SCFAs): butyrate, propionate, and acetate. 

SCFAs result from the fermentation of indigestible carbohydrates. Butyrate is a primary energy source for intestinal epithelial cells (gut guardians), helps support intestinal barrier function, and boosts immunity and intestinal homeostasis.


SCFAs have an anti-inflammatory effect on the gut and the rest of the body. As SCFAs pass through the gut barrier and into blood circulation, they confer an anti-inflammatory effect on organs and tissues such as the liver, lungs, fat tissue, and the brain.

Dysbiosis and gut health

If the composition of the intestinal microbiota tips in favor of bad bacteria, it’s known as dysbiosis. Dysbiosis alters the delicate exchange of resources between the host and gut microbes and can start a cascade of events that might later present as a range of health disorders such as metabolic syndrome, autoimmunity, or neurodegenerative diseases such as Parkinson’s.

For instance, a weak gut barrier allows toxic microbial cell fragments such as lipopolysaccharides (LPS) to leak into the bloodstream, starting a chain of pro-inflammatory events as immune cells mount a defense against a toxic foreign substance in the blood.

Recent research highlights LPS as a source of chronic inflammation that can lead to a host of metabolic and neurodegenerative concerns including type 1 diabetes and Alzheimer’s. 


While acute (short-term) inflammation is a protective mechanism, chronic low-grade intestinal inflammation can lead to sustained harm to healthy tissue and might cause conditions such as irritable bowel syndrome (IBD), diabetes, and other chronic diseases.

Probiotic supplements can potentially help shift the balance of the gut microbiome and circulating LPS in the blood. A recent study published in the Journal of Biotechnology and Biomedicine assessing the effects of BiotiQuest™ Sugar Shift® over twelve weeks showed significant reductions in circulating LPS and insulin levels. 

A healthy immune system — How does it work?

A balance between inflammatory and anti-inflammatory immune responses is essential for a healthy immune system. While the immune system must fight off bad bacteria promptly via an inflammatory immune response, regulatory or anti-inflammatory immune responses are necessary to help taper off inflammation and protect against damage to healthy tissue.

Innate and adaptive immunity are two types of immune responses that work together to help maintain immune health. 


What are innate and adaptive immune responses?

The immune system provides several layers of protection and can be divided into two different types: innate and adaptive immunity. Innate immunity stands as the first line of defense against pathogens. It comprises physical and chemical barriers including skin and mucous membranes such as the gut mucosal wall as well as different immune cells such as dendritic cells, neutrophils, and macrophages that act to activate the adaptive immune response. 

Innate immunity can physically restrict pathogens' movement or tag them with molecules that activate adaptive immunity. Adaptive immune response serves two functions, the first is to mount a pathogen-specific attack and the second is to create memory cells that allow your immune system to react much faster in case of a future encounter.

Gut immune system and gut microbiome

Your gut houses up to 70% of the immune system as it deals with an ever-changing passage of foreign substances, including food and pathogens. Gut immunity has both innate and adaptive immunity as gut mucosal wall and gut-associated lymphoid tissues (GALTs). 

The gut microbiome plays an irreplaceable role in the development, maturation, and maintenance of the different layers of gut immunity. Among these microorganisms, probiotics or beneficial gut bacteria confer many health benefits like maintaining the integrity of the gut wall, supporting a diverse gut flora, optimizing digestion, metabolizing and absorbing nutrients, and regulating immune function. 

Gut mucosal immune system

The gut's innate immune response or mucosal immunity is a gel-like substance produced by intestinal goblet cells. The mucous layer lines the intestinal epithelial cells and prevents gut bacteria from coming in direct contact with the intestinal epithelium and triggering an adaptive immune response.

The gut wall includes two layers of mucous membranes — the inner and outer mucin layers. The inner mucin layer doesn't allow entry to bacteria, whereas the outer mucin layer houses antimicrobial peptides, secretory immunoglobulin A (SIgA), and mucous-associated beneficial bacteria that restrict the growth of bad bacteria and inhibit contact with intestinal epithelial cells. 

The state of the mucous membrane depends on mucin production by goblet cells, regular wear and tear, and degradation by mucous-associated beneficial bacteria.

Adaptive immune system

Immune regions known as gut-associated lymphoid tissues or GALTs line your gastrointestinal tract. These regions act as little factories where immune cells like B cells and T cells develop and mature. GALTs are also responsible for the optimum production of SIgA (secretory Immunoglobulin A), an essential antibody that supports a healthy and diverse gut microbiome.

Specialized immune cells capture pathogens or bacterial fragments and carry them to immune cells, initiating a protective pro-inflammatory immune response that protects you from infections.

Research suggests newborns and germ-free mice have an underdeveloped adaptive immune system that matures and develops upon exposure to helpful or commensal bacteria. Newborn gut health benefits from human milk oligosaccharide (breast milk) as it feeds beneficial strains of bifidobacteria like B. infantis. B. infantis confers an anti-inflammatory effect on the gut and helps with the development and maturation of the adaptive immune response. 

Probiotics and the Immune System

Probiotics are live microorganisms that may have beneficial effects on your health and support immune function. Probiotic strains such as L. plantarum and L. reuteri produce antimicrobial compounds called plantaricin and reuterin that act to inhibit the growth of pathogenic competitors.

Probiotic Bifidobacterium and Lactobacillus strains such as B. bifidum and L. acidophilus produce short-chain fatty acids including butyrate, acetate, and propionate that have immunomodulatory or tolerance effects on the immune system which helps limit inflammation in the body.


The link between probiotics and immune function

As your gut faces constant exposure to external stimuli, it has developed immune responses that help foster the growth of beneficial bacteria while simultaneously protecting itself against harm from pathogenic bacteria.

One such immune mechanism is the abundance of SIgA in the gut. SIgA is an antibody that attaches to gut bacteria and keeps them away from the intestinal epithelium and underlying immune cells. Research has found an increase in SIgA production following probiotic administration that includes probiotic microbes such as B. bifidum.

Specific probiotic bacteria strains such as L. acidophilus have been associated with increasing the performance of tight junction proteins. Tight junction proteins act as the glue between intestinal epithelial cells, and a healthy tight junction protein network prevents bacterial endotoxins such as LPS from leaking through the intestinal barrier.


Probiotics and a weakened immune system

A course of antibiotics may follow an infection, illness, or surgery. A common after-effect of antibiotic treatments is antibiotic-associated diarrhea (ADD), as antibiotics wipe off beneficial bacteria, allowing pathogenic bacteria like C. difficile to proliferate.

According to a systemic review and meta-analysis, the use of probiotics to prevent antibiotic-associated diarrhea reduced the risk of ADD by 51%. Probiotics in the review included Streptococcus and Lactobacillus strains like S. thermophilus, L. rhamnosus, and L. acidophilus.

Probiotics are associated with a host of beneficial effects such as reduced inflammation in the gut, a stronger immune system, and improved digestion. 

Do probiotics impact inflammation?

Immune homeostasis is the balance between inflammatory immune responses and regulatory anti-inflammatory responses. Regulatory T cell (Treg) is a type of immune cell that has an anti-inflammatory effect and works to counterbalance inflammation. 

A healthy and diverse gut microbiome has been associated with the maintenance of immune homeostasis and the proliferation of Treg cells and anti-inflammatory signaling proteins.

If pro-inflammatory pathways surpass anti-inflammatory pathways, it might cause autoimmune and inflammatory conditions such as allergies, MS, type 1 diabetes, and IBD.

Do probiotics boost immune function?

A diverse gut microbiome confers the ability to tolerate harmless food antigens and bacterial debris. Beneficial bacteria affect gut health by limiting and restricting the growth of pathogenic bacteria and thus reducing pro-inflammatory bacterial endotoxic triggers such as LPS.

The production of beneficial metabolites such as SCFAs has an anti-inflammatory effect, which is essential to keep the immune system in equilibrium. In the absence or reduction of anti-inflammatory mechanisms, prolonged inflammation will cause persistent damage to healthy tissue.

Fermented foods like homemade yogurt and kimchi and probiotic supplements rich in specific beneficial bacterial strains that support SCFA production and antimicrobial compounds can be great ways to support your immune system.


Front view of glass bottle with 60 capsules of Ideal immunity.Our Ideal Immunity® formula targets the way your gut microbiome interacts with your immune system. It helps fortify mucosal surfaces, fights off pathogens, reduces toxic load, and gives your body a boost so you can feel good.

Or, if you’re looking to support your gut microbiome after a course of antibiotics, Antibiotic Antidote® was specifically developed to create the right environment to enable friendly bacteria to flourish again after taking antibiotics. As your body rebuilds its ecosystem, it targets free radicals generated by antibiotic use, strengthens the mucosal lining, and balances gut pH.

In conclusion, your gut acts as the command center for your immune responses as it houses over 70% of your immune system and the strength of your immune system determines your health. Your gut microbiome and immune system have co-evolved to support and benefit from each other. 

A balanced and diverse gut microbiome benefits your body’s immunity, brain function, and digestion. Beneficial bacteria not only support the growth and maintenance of the immune system but they also out-compete pathogenic bacteria before they can find a foothold in the gut and cause disease. 

With gratitude,

Martha Carlin photo Martha Carlin, is a “Citizen Scientist”, systems thinker, wife of Parkinson’s warrior, John Carlin, and founder of The BioCollective , a microbiome company expanding the reach of science and BiotiQuest, the first of it’s kind probiotic line. Since John’s diagnosis in 2002, Martha began learning the science of agriculture, nutrition, environment, infectious disease, Parkinson’s pathology and much more. In 2014, when the first research was published showing a connection between the gut bacteria and the two phenotypes of Parkinson’s, Martha quit her former career as a business turnaround expert and founded The BioCollective to accelerate the discovery of the impact of gut health on all human disease. Martha was a speaker at the White House 2016 Microbiome Initiative launch, challenging the scientific community to “think in a broader context”. Her systems thinking background and experience has led to collaborations across the scientific spectrum from neuroscience to engineering to infectious disease. She is a respected out of the box problem solver in the microbiome field and brings a unique perspective to helping others understand the connections from the soil to the food to our guts and our brains.

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