Your gut and immune system are in constant contact, and researchers are learning how that link may relate to food allergies and autoimmune disease. Here’s what the science shows so far, and what it doesn’t.
The gut and immune system communicate daily through the gut-immune axis.
The gut microbiome helps shape immune development, immune tolerance, and the gut barrier.
Studies have found differences in the gut microbiome in people with food allergies and autoimmune disease.
Researchers are studying whether these differences affect immune function, but current findings don’t show that microbiome differences cause either condition.
A varied, fiber-rich diet can support your gut microbiome and overall health.
A microbiome test shows which microbes live in your gut and what they may be able to do, but it can’t diagnose an autoimmune disease or food allergy.
Your gut is home to trillions of microbes, and many of your immune cells live there, too. In your gut microbiome, these immune cells learn what’s friendly, like food and friendly bacteria, and what’s worth fighting, while your microbes respond to the immune system in turn.Â
This two-way relationship, called the gut-immune axis, helps shape your health from your first days of life onward. Researchers are now exploring how the gut microbiome may be linked to immune-related conditions at every age, including autoimmune diseases and food allergies.
If you’ve taken a Tiny Health test, you can see how this plays out in Gut-Body Connections, the interactive feature in your report that links patterns in your gut microbiome to different body systems.
What is the gut-immune axis?
The gut-immune axis describes the two-way connection between your gut and immune system.
Your digestive tract does much more than just digest food. It is also one of the body's main points of contact with the outside world. Every day, food, microbes, and other substances enter your body through the digestive tract. Your immune system decides what’s harmless and what may be a threat.
The gut microbiome, gut barrier, and immune system all play a role in these decisions. Research suggests that signals from gut microbes can affect the immune system, while the immune system can also shape the gut [1], [2].
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Gut element
Definition
Immune role
Gut microbiome
The community of microbes living in the gut
Communicates with immune cells and produces compounds that can affect immune activity
Gut barrier
The lining of cells that covers the inner surface of the gut
Helps control what passes from the gut into the body
Gut immune system
Immune tissue in the gut wall, home to a large share of the body’s immune cells
Monitors the digestive tract and responds to potential threats
Mucus layer
A gel-like coating on top of the gut barrier
Keeps gut microbes away from intestinal cells
Microbial compounds
Substances gut microbes produce when they break down food and other substances, such as short-chain fatty acids (SCFAs)
Can calm or activate immune responses
This close relationship means that changes in one part of the system may affect the others. At the same time, illness, diet, medications, and other factors can also affect the gut microbiome [1], [2].
How does the gut microbiome affect the immune system?
Your immune system constantly communicates with the microbes living in your gut. The gut barrier helps manage this by keeping gut contents separate from your gut tissues, while still letting your immune system check in on microbes and food in a controlled way.
How microbes talk to immune cells
Your immune system senses gut microbes in two main ways [1]:
Recognizing microbial parts: Cells in the gut lining and immune cells have sensors that detect common parts of microbes, like pieces of bacterial cell walls. Steady, low-level signals from normal gut microbes help keep the gut barrier strong and the immune system ready.
Responding to microbial compounds: Gut microbes make compounds that reach gut tissue and act as signals. For example, short-chain fatty acids, like butyrate, are made when microbes break down fiber. They feed the cells that line the gut and help build regulatory T cells, a type of immune cell that calms immune responses.
Helping the immune system learn
The gut microbiome plays an important role in immune development. Signals from gut microbes help immune cells develop and learn to tolerate friendly substances while responding to threats from invaders [1]-[3]. This process starts early. In infancy, the first microbes to settle in the gut help train the growing immune system [2].
Learning tolerance is especially important for food.
When you eat, your immune system encounters proteins from food. Ideally, it learns that these proteins are safe. This process is called oral tolerance.
Gut microbes may support oral tolerance in several ways [3]:
Regulating immune cells: Microbial compounds can influence immune cells, helping to support immune responses.
Supporting the gut barrier: A healthy intestinal lining helps control how substances come into contact with immune cells.
Producing helpful compounds: Some gut microbes produce metabolites like short-chain fatty acids that may influence the immune system.
These interactions are one reason researchers are interested in the gut microbiome’s role in immune diseases.Â
Supporting the gut barrier
The gut barrier acts like a gatekeeper. It lets nutrients pass into the body while keeping unwanted substances out.
The gut microbiome interacts closely with this barrier. Some gut microbes and their metabolites can support the gut, while microbial signals can also influence immune activity [1], [3].
How the immune system shapes the microbiome
Immune cells in the gut wall release an antibody called IgA into the gut, which is the immune system’s main defense along the gut lining. IgA sticks to some bacteria and helps control where they live and which ones grow. Cells in the gut lining also release proteins that help keep microbes away from the gut wall [1], [2].
The gut-immune axis and autoimmune disease
Autoimmune diseases happen when the immune system loses the ability to tell the difference between foreign invaders and the body’s healthy tissues. As a result, it attacks those tissues by mistake.
Researchers are increasingly studying the gut microbiome in autoimmune disease. Studies have found differences in the microbiomes of people with autoimmune conditions compared with people without them [4], [5]. These findings are important, but they do not show that a microbiome difference causes autoimmune disease. Genetics, hormones, environmental exposures, medications, diet, and immune activity can all influence both the disease and the microbiome.
The relationship between the microbiome and autoimmune diseases is stronger for some conditions than others. One example is systemic lupus erythematosus, commonly called lupus. Lupus is a chronic autoimmune disease in which the immune system attacks the body's tissues.
Recent studies have found lower microbial diversity in people with lupus, with differences in some bacterial groups, including enriched Streptococcus and depleted Bifidobacterium [4], [6]. The relationship between lupus and the gut microbiome is still being studied. It’s not yet clear if differences in the gut microbiome contribute to lupus, result from the condition, or are influenced by other factors.
The gut-immune axis and food allergies
Food allergies happen when the immune system reacts to a protein in a food as if it were harmful. Both genes and environment play a role in food allergies, and researchers are now looking at the role of the gut microbiome. Studies have found differences in the gut microbiome of children with food allergies, including allergies to egg and peanut [7], [8].
Researchers are especially interested in how the gut microbiome may affect immune tolerance. When the immune system learns to tolerate food proteins, it sees them as safe instead of overreacting to them [3], [7]. This research matters most early in life, when the gut microbiome and immune system are both growing and changing quickly.
Researchers are looking at connections between the gut microbiome and two types of food allergies: food protein-induced allergic proctocolitis (FPIAP) and cow’s milk protein allergy (CMPA).
FPIAP is a non-IgE-mediated food allergy that mostly affects young babies. Non-IgE-mediated food allergies are different from IgE-mediated food allergies because they don’t usually cause fast symptoms like hives, swelling, wheezing, or anaphylaxis [9]. CMPA, on the other hand, is an immune reaction to proteins in cow’s milk. It is one of the most common food allergies in babies and affects about 3% of children in their first year [10], [11]. CMPA can cause stomach, skin, and other symptoms. Some forms involve IgE antibodies, which can cause a fast allergic reaction. Other forms are slower and don’t involve IgE [12].
Some studies have found differences in the gut microbiome of babies with FPIAP compared with babies without it. A 2023 study that followed babies over time found differences in overall gut microbes and lower levels of Bifidobacterium in babies who may have had FPIAP [13]. A 2022 study also found other differences in babies with FPIAP, such as higher levels of Enterobacteriaceae [14].
Studies have also found differences in the gut microbiome of babies with CMPA. For example, a 2022 study found differences compared to babies without allergies, specifically a loss of beneficial Bifidobacterium [15].
A baby’s gut microbiome changes quickly during the first year of life. It is shaped by things like breastfeeding or formula feeding, starting solid foods, how the baby was born, antibiotics, age, and other things in the baby’s environment [14], [16]. Because of this, it can be hard to tell whether microbiome differences are linked to food allergies or to these other factors.
What gut microbiome patterns are researchers studying?
Researchers are looking at several features of the gut microbiome when studying immune health.
Microbial diversity
Microbial diversity refers to how varied the microbial community is.
Several studies have found lower measures of microbial diversity in people with lupus [4], [17]. Research in FPIAP has also found differences in microbial diversity, although findings vary between studies [13], [14].
Microbial composition
Researchers also look at which microbes are present and how much of each microbe is found.
For example, studies of lupus have found differences in bacterial groups, including lower abundance of Bifidobacterium, Collinsella, and Ruminococcus and higher abundance of Enterobacteriaceae [4], [5], [17]. This pattern represents a loss of beneficial microbes and an overgrowth of potential pathogens.Â
Studies of FPIAP have reported differences involving lower abundance of Bifidobacterium and higher abundance of Escherichia coli, alongside other bacterial groups [13], [14], [16].
Functional microbiome potential
Your microbes also carry genes that allow them to perform different functions.
Researchers can study these genes to understand what the microbiome may be capable of doing, such as breaking down dietary fiber or producing microbial compounds that interact with the gut and immune system.
This is especially interesting in food allergy research. The 2026 FPIAP study, for example, found differences in microbial pathways related to short-chain fatty acid production [16]. Short-chain fatty acids play an important role in supporting the immune system by strengthening the gut barrier and regulating early immune responses.Â
Is "leaky gut" connected to immune health?
You may have heard the term "leaky gut." Scientists generally refer to this as increased intestinal permeability.
The gut barrier is designed to control what moves from the digestive tract into the body. When this barrier becomes more permeable, substances can cross the intestinal lining more easily. This can influence immune activity and contribute to inflammation.
Research has found connections between changes in intestinal permeability, inflammation, and immune-related conditions. The gut microbiome also interacts with the cells and compounds that help maintain the gut barrier [1], [3].
But the idea that "leaky gut causes autoimmune disease" is an oversimplification.
Researchers are still trying to determine whether changes in intestinal permeability are a cause, a result of disease, or one part of a larger cycle involving the microbiome and immune system.
The gut barrier is therefore an important part of the gut-immune axis, but it is only one piece of a much larger system.
How can you support gut and immune health?
You cannot control every factor that affects your immunity or gut microbiome, but everyday habits can support a healthy gut environment. Genetics, age, medications, environment, and many other factors all matter.
Some gut microbes turn fiber into short-chain fatty acids, which can interact with gut cells and immune cells [3]. There is no single food or superfood that can fix your microbiome. Eating a varied diet gives your gut microbes a range of nutrients to work with
Avoid unnecessary food restriction
Removing foods without a medical reason can make it harder to get a wide range of nutrients and may reduce dietary variety.
If you or your child has a suspected food allergy, FPIAP, or CMPA, do not make major dietary changes without guidance from a healthcare professional. Infants and young children have specific nutritional needs, and food allergies require appropriate diagnosis and management.
Together, these connections make up what Tiny Health calls Gut-Body Connections, a proprietary interactive body map in your Results portal, linking your microbiome patterns to your immune system and other body systems. You can find this feature on the home screen and the Conditions page.
Each connection offers another way to study how the gut microbiome may relate to different aspects of your health. The science and technology behind how these connections are developed are explained in our deeper Gut-Body Connections guide.
A personalized exploration into Gut-Body Connections
Tiny Health’s Adult Gut Health Test uses deep shotgun metagenomics to analyze the microbes in your gut, including species and, in some cases, strains. It can also provide information about functional potential, or what the microbes in your microbiome may be capable of doing based on the genes they carry.
In the Gut-Body Connections section of your report, Tiny Health combines published scientific research with its own metagenomic data to identify microbiome patterns that may connect to different areas of health. These connections describe research associations, not diagnoses. A microbiome test cannot tell you that you have lupus, a food allergy, FPIAP, or CMPA.
Instead, it can give you a detailed picture of your gut microbiome and help you understand how the microbes and functions found in your gut relate to areas of health being studied by researchers.
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What you should know
Frequently Asked Questions: Gut-immune axis
What is the gut-immune axis?
The gut-immune axis is the two-way connection between your gut and immune system. Your gut microbiome, gut barrier, and immune cells communicate with each other and help regulate immune activity [1], [2].
How does the gut microbiome affect the immune system?
Gut microbes can interact with immune cells, support the gut barrier, and produce compounds that affect immune activity. These interactions may help the immune system develop tolerance to harmless substances, including foods [2], [3].
Can gut health cause autoimmune disease?
There is not enough evidence to say that gut health alone causes autoimmune disease. Studies have found differences in the gut microbiome of people with conditions such as lupus, but genetics, hormones, environment, medications, and other factors also play a role [4], [5].
Is there a connection between the gut microbiome and food allergies?
Yes. Research has found differences in the gut microbiome of people with food allergies and suggests that gut microbes may influence immune tolerance to food. Researchers are still studying exactly how these relationships work [3], [7], [8].
Is FPIAP the same as CMPA?
No. FPIAP is a specific type of delayed, non-IgE-mediated food allergy that mainly affects the digestive tract in infants. CMPA is a broader term for an immune reaction to cow's milk proteins and can involve both IgE-mediated and non-IgE-mediated reactions [9], [12].
Can a gut microbiome test diagnose a food allergy?
No. A microbiome test can identify microbes and microbial functions in the gut, but it cannot diagnose a food allergy, FPIAP, or CMPA.
Can a gut microbiome test diagnose lupus?
No. A microbiome test is not a diagnostic test for lupus. While research has found microbiome patterns associated with lupus, these findings are still being studied and cannot replace medical testing or evaluation [4], [5], [17].
Can probiotics improve immune health?
Some specific probiotic strains have been studied for immune and allergy-related outcomes. However, effects can vary depending on the strain, condition, and person. There is no single probiotic that is proven to improve immune health for everyone.
What are Gut-Body Connections?
Gut-Body Connections is Tiny Health's framework for exploring research connections between the gut microbiome and different parts of the body, including the brain, skin, and immune system. The gut-immune axis is one part of this broader framework.
When to seek medical attention
A change in your gut microbiome is not a diagnosis.
If you or your child has ongoing digestive symptoms, blood in the stool, poor growth, repeated allergic reactions, trouble breathing, swelling, or other symptoms, talk with a healthcare practitioner.
For infants with suspected FPIAP or CMPA, medical guidance is especially important before removing foods or changing feeding.
A microbiome test can provide information about the gut, but it should not replace medical evaluation, allergy testing when appropriate, or treatment prescribed by your healthcare team.
Trust your gut.
Get to know your microbes with an easy, 5-minute at-home test from Tiny Health. Unlock deep gut health insights and personalized recommendations for your diet, supplements, and lifestyle.
Dr. Hannah Sturgeon, a Neuroscience Ph.D. from Georgia State University, specializes in microbiome research with expertise in early gut-brain-immune development.
