The answer to a reactive gut isn’t simply eliminating certain foods, says nutritional therapist Georgia Lennard. It’s learning how to nurture a more resilient gut microbiome—and, in turn, a more robust immune system
We have never been more interested in gut health. Supermarket shelves are filled with probiotic yogurts and fermented foods, while social media encourages us to drink kefir and kombucha to feed our gut microbes. The message seems simple: Nurture your microbiome, and better health will follow.
Yet in clinical practice I have noticed something that initially seemed contradictory. Many people begin introducing these supposedly healthy foods only to find that they feel no different—or, in some cases, temporarily feel worse. Fermented foods trigger bloating, headaches, itching or digestive discomfort.
Others experience no noticeable improvement at all. Understandably, this leaves people wondering whether these foods are as healthy as they are claimed to be.
But instead of asking whether kefir, sauerkraut or kombucha is healthy, perhaps we should ask why some people appear to have lost the ability to tolerate foods that have nourished human populations for generations. Could it be that the problem is not the food itself but the biological environment into which it is introduced?
Have we become less tolerant of many of the things that once helped keep us healthy? Pollen, diverse plant foods, environmental microbes and even our own commensal bacteria now appear to provoke exaggerated immune responses in many people.
While genetics undoubtedly play an important role, research over the past two decades suggests that modern lifestyles—including changes in diet, environmental microbial exposure and the cumulative effects of the exposome (environmental exposures throughout life)—may also have altered one of our most important biological partners: the gut microbiome.1
Perhaps many of the chronic symptoms increasingly affecting modern societies are not the result only of new triggers appearing around us but of a gradual loss of the biological resilience that once allowed us to live alongside them.
Trillions of microorganisms live within and on us, forming a dynamic ecosystem that works in partnership with the body. Together they help digest food, protect against pathogens, support the gut lining and influence many aspects of metabolism and human health. Far from being passive passengers, these microorganisms perform essential functions that our own bodies cannot carry out alone. Collectively, they are known as the human microbiome.
Humans and their gut microbes have evolved together over millions of years in a mutually beneficial relationship. While we provide microbes with a place to live and a constant supply of nutrients, they contribute to processes that help maintain our health throughout life. Research increasingly suggests this partnership is shaped continuously by factors such as diet, medications, infections, stress and the wider environment, making the microbiome a remarkably dynamic part of our biology.
One of the ways the microbiome influences health is through the production of short-chain fatty acids such as butyrate, acetate and propionate. These microbial metabolites help maintain the intestinal barrier, regulate inflammatory pathways and support immune tolerance, providing one of the key biological mechanisms through which gut microbes communicate with the body.2
Perhaps the microbiome’s most remarkable role, however, is not in digestion but in educating the immune system. Understanding how gut microbes help teach the immune system to distinguish between harmless exposures and genuine threats has transformed the way researchers think about health—and forms the basis of one of the immune system’s most remarkable abilities: immune tolerance.
During early life, gut microbes help teach immune cells the difference between harmless substances—such as food proteins, beneficial bacteria and everyday environmental exposures—and genuine threats that require a defensive response. The education continues throughout life, helping maintain an immune system that responds proportionately rather than excessively.
This finely tuned process is known as immune tolerance. When immune tolerance functions well, the immune system responds appropriately to challenges while ignoring harmless exposures.
When this balance becomes disrupted, however, immune responses may become exaggerated. Rather than responding proportionately, the immune system may begin reacting more strongly than necessary, contributing to allergic and inflammatory conditions.
Hay fever is a good example. Pollen itself is harmless, yet in susceptible people, the immune system treats it like a dangerous invader, triggering the release of inflammatory mediators such as histamine.
The result is the familiar combination of itchy eyes, sneezing, congestion and a runny nose. Similar patterns of immune overreactivity may underlie food allergies, eczema and other allergic conditions, although the specific triggers and symptoms vary considerably from person to person.
What causes this loss of tolerance is complex and differs among individuals. Genetics, environmental exposures and the integrity of the gut barrier, together with the composition and function of the gut microbiome, all appear to contribute. Rather than being due to a single cause, it is more helpful to think of immune tolerance as continually shaped by the conversation between our genes, our environment and the trillions of microbes living within us.
One little girl I met had eczema that first appeared after she received antibiotics at just eight weeks of age. Over the months that followed, she developed disturbed sleep, recurrent infections and persistent constipation. The antibiotics were not necessarily the cause of her eczema, but they pointed to what might have been happening within her developing gut microbiome and immune system during such a critical window of early-life immune development.
Rather than focusing solely on calming her skin, we began exploring the health of the systems that help regulate immune responses in the first place. Her plan involved targeted probiotic support, gradually introducing a more diverse range of foods and supporting her nervous system with lots of closeness and connection with her mother.
Her improvement was gradual but dramatic over around six months. She is now almost completely eczema-free, with just the occasional dry patch appearing from time to time.
For most of human history, people lived in close contact with the natural world. We spent far more time outdoors, and encountered a rich diversity of environmental microbes through soil, plants and animals. We also ate diets that were naturally higher in fiber and considerably less processed than those consumed today. While life expectancy was shorter and infectious diseases posed significant risks, our microbial environment looked very different from that of industrialized societies today.
Over the past century, our lifestyles have changed dramatically. Antibiotics have transformed modern medicine and saved countless lives. Yet research shows that antibiotics can also alter the composition of the gut microbiome, particularly during early life, when the microbial community is still developing.
Most people recover well after a course of antibiotics, but repeated exposure or disruption during critical periods of immune development may have longer-lasting consequences for some people.3
Antibiotics are only one piece of the puzzle. Modern diets are often lower in fiber and plant diversity, providing less nourishment for many beneficial gut microbes.
Chronic psychological stress, inadequate sleep, reduced exposure to nature, increasing urbanization and other aspects of modern living have also been associated with changes in the composition and function of the gut microbiome. These influences form part of what researchers sometimes refer to as the exposome—the sum of the environmental factors that shape our biology throughout life.
In a fascinating Finnish study, researchers transformed urban daycare playgrounds by introducing biodiverse forest floor, natural vegetation and planting boxes. Within just four weeks, children exposed to these biodiverse environments showed measurable changes in both their skin and gut microbiota, together with favorable changes in markers of immune regulation.4
The study provides compelling evidence that relatively small changes in our everyday environment may influence the microbes we live alongside. This in turn affects the microbial composition of the gut and the way the immune system develops.
Individually, each of these influences may seem relatively small. Collectively, however, they may help explain why many people today appear to be carrying a less diverse and potentially less resilient gut microbiome than previous generations.
Studies such as these suggest that our microbiome is not fixed but continually responds to the environments in which we live. Since the gut microbiome plays an important role in immune regulation, changes in microbial diversity and microbial function may also influence immune resilience in susceptible people.
Supporting microbial diversity and function through a varied, fiber-rich diet, restorative lifestyle practices and regular contact with biodiverse natural environments may represent one practical way of supporting long-term immune resilience.
One of the most misunderstood consequences of microbial imbalance involves histamine. Histamine is often portrayed as the villain behind allergic symptoms, yet histamine itself is not harmful. In fact, it’s an essential signaling molecule involved in many normal physiological processes, including immune defense, stomach acid production, wound healing and communication within the nervous system.5
The challenge arises when histamine accumulates faster than the body is able to break it down or regulate it. When this happens, some people may experience symptoms including itching, flushing, headaches, nasal congestion, digestive discomfort, disturbed sleep or skin reactions. These symptoms are often referred to collectively as histamine intolerance.
The gut microbiome appears to be one of the factors that may influence this balance. Some gut bacteria can produce histamine, while others contribute to its breakdown or help maintain the balanced microbial ecosystem in which histamine regulation occurs.
Beyond histamine metabolism itself, beneficial gut microbes also produce short-chain fatty acids that help maintain the intestinal barrier and regulate immune responses, highlighting that microbial function is just as important as microbial diversity in maintaining immune resilience. A healthy gut microbiome therefore influences far more than digestion; it contributes to the broader regulation of immune and inflammatory responses.6
Research suggests that reduced histamine degradation capacity (when the body is less able to break down histamine efficiently) has been identified in a subgroup of patients with atopic eczema, illustrating that altered histamine regulation may contribute to symptoms in some people.7
This helps explain why health advice cannot always be universal. Fermented foods, for example, are frequently recommended because they can provide beneficial microbes and fermentation products that support gut health. However, many fermented foods also naturally contain histamine.
For someone with a resilient gut microbiome and a well-regulated immune system, these foods are often well tolerated. For someone whose microbiome has become disrupted or whose ability to regulate histamine is temporarily impaired, exactly the same foods may provoke uncomfortable symptoms.
This is something I see regularly in clinical practice. Many clients arrive feeling confused because they have been diligently eating foods widely promoted as supporting gut health—such as kefir, kombucha or sauerkraut—yet they report feeling worse rather than better.
Rather than concluding that these foods are unhealthy, we ask whether their current gut microbiome and immune system are ready to tolerate them. In many cases, the long-term goal is not lifelong avoidance but rebuilding resilience so these foods can eventually be enjoyed without provoking symptoms.
Instead of simply eliminating foods, it’s important to look at why a person’s tolerance may have changed. Supporting gut health, restoring microbial diversity and microbial function where appropriate, and taking an individualized approach to nutrition may help improve tolerance over time.
Another important factor influencing microbial resilience is the integrity of the intestinal barrier.
Although often thought of simply as a digestive organ, the gut lining also acts as a highly selective barrier between the outside world and the bloodstream, allowing nutrients to pass through while helping to keep microbes, toxins and other potentially harmful substances under control. Beneficial gut bacteria help maintain this barrier through a variety of mechanisms, including the production of short-chain fatty acids such as butyrate, which nourish intestinal cells, strengthen tight junctions and support normal immune regulation.
When this barrier becomes compromised, communication between the gut microbiome and the immune system may also become altered. Increased intestinal permeability—sometimes referred to as “leaky gut”—has been associated with increased immune activation and inflammation in a range of chronic conditions.8
As inflammatory signaling increases, the consequences may not remain confined to the digestive tract. For some people, symptoms appear predominantly in the gut, while others experience changes affecting the skin, joints, respiratory system or brain.
The encouraging news is that resilience can often be improved. While no single approach suits everyone, several common principles emerge repeatedly from both research and clinical practice.
Reduce the inflammatory burden. This may involve temporarily reducing foods that appear to aggravate symptoms while the gut and immune system recover. Some people may need to reduce intake of high-histamine foods (see below).
This is not a lifelong restriction, only a strategic period of support while underlying resilience is rebuilt. The aim is to provide the body with an opportunity to regain balance before foods are gradually reintroduced where appropriate.
Increase microbial diversity and function. A diverse gut microbiome is consistently associated with greater resilience, but equally important is what those microbes actually do. Beneficial fiber-fermenting bacteria produce short-chain fatty acids that help maintain the intestinal barrier, regulate immune responses and support immune tolerance.
Rather than searching for individual “superfoods,” it is often more helpful to focus on eating a wide variety of colorful plant foods across the week. Vegetables, herbs, spices, nuts, seeds, legumes (where tolerated) and berries all provide different fibers and polyphenols that nourish different members of the microbial community. The goal is not simply to increase the number of microbes but to support a healthier and more resilient microbial ecosystem.
Introduce change gradually. Sometimes foods intended to support the microbiome need to be introduced slowly, particularly when symptoms are severe or long-standing. Supporting gut barrier integrity may also form an important part of the picture. Adequate protein (aim for a good source of protein at every main meal), key vitamins and minerals, restorative sleep, effective stress management and nourishing whole foods all contribute to an internal environment in which both the gut lining and the microbiome can recover (see 7 ways to build gut resilience, below).
There is no such thing as an average microbiome. Every person’s microbial ecosystem is unique, shaped by genetics, birth history, diet, medications, environmental exposures, illness and countless other influences throughout life.
This helps explain why the same intervention can produce very different results in different people. One person may thrive on fermented foods, while another initially finds them difficult to tolerate. One individual benefits from a particular probiotic, while another notices little difference.
Advances in gut microbiome testing are allowing clinicians to move beyond educated guesswork. Full-resolution metagenomics provides a detailed picture not only of microbial diversity but also of microbial function, together with the relative abundance of key bacterial species. This enables practitioners to build more personalized strategies based on an individual’s biology rather than relying solely on general recommendations.
So instead of simply prescribing a probiotic or recommending a particular diet, we can look at what a person’s individual microbiome actually needs—which beneficial bacteria are missing, which bacteria have overgrown, what is happening with microbial diversity, and how this all fits with a person’s symptoms, diet and medical history.
This simple shift reflects one of the biggest changes taking place in nutritional science: moving away from one-size-fits-all advice toward genuinely personalized care.
This is why it can be so valuable to work with a functional medicine practitioner who can tailor tests, treatments and lifestyle advice to suit you and your needs (you can find one near you via the Institute for Functional Medicine at ifm.org).
Gut health is not built through supplements alone. While targeted nutritional support can certainly have its place, the gut microbiome is continually shaped by the way we live. Every meal we eat, every night of sleep, every stressful period, every walk outdoors and every interaction with the natural world contributes to the environment in which our microbes live.
Human beings evolved in close relationship with nature and with each other. For most of our evolutionary history, daily life involved regular contact with soil, plants, animals and an extraordinary diversity of environmental microorganisms. Emerging research suggests that reconnecting with biodiverse natural environments may influence not only our well-being but also the microbial communities living on and within us.
In the Finnish biodiversity study discussed earlier, relatively simple changes to children’s everyday play environments altered both the skin and gut microbiota while improving markers of immune regulation within just four weeks. Together with growing evidence that our wider environmental exposures help shape both the gut microbiome and immune health, these findings remind us that the environments we inhabit continue to influence the biology we carry within us.
The same principle extends beyond nature. Regular physical activity has been associated with a healthier and more resilient gut microbiome, while restorative sleep, effective stress management and meaningful social connection all influence the complex relationship between the gut microbiome, the immune system and overall health through the gut–brain axis.
None of these influences acts in isolation. Rather, they work together to create an internal environment that supports resilience over time.
Perhaps this is one of the most encouraging messages emerging from microbiome research. Many of the practices associated with supporting a healthier microbiome are neither expensive nor complicated (see 7 ways to build gut resilience, below). They are fundamental aspects of human biology that have shaped our relationship with the microbial world for thousands of years.
Rather than searching endlessly for the next miracle supplement or health food, perhaps we should first ask whether we are consistently giving our bodies—and our microbes—the conditions they have evolved to thrive in.
Perhaps nowhere is the relationship between the gut microbiome and the immune system more visible than in childhood eczema.
Eczema has traditionally been viewed as a disease of the skin, yet many families describe patterns that suggest something more may also be happening beneath the surface. As our understanding of the gut microbiome has grown, researchers have increasingly explored how the microorganisms living within the gut may influence immune regulation and, in turn, inflammatory conditions affecting distant organs, including the skin.1
Parents often tell me that their child’s eczema worsened after repeated courses of antibiotics, following a viral illness, during periods of poor sleep or alongside increasing food sensitivities. Many children also experience digestive symptoms such as constipation, bloating or abdominal discomfort, while others develop hay fever, asthma or recurrent infections. A question I always ask is, why has this child’s immune system become so reactive?
Several studies have reported differences in the gut microbiome of infants and children with atopic dermatitis compared with healthy controls, including lower microbial diversity, alterations in bacterial composition and reductions in beneficial bacteria associated with immune regulation.
Lower microbial diversity during the first months of life has also been associated with an increased risk of developing eczema later in infancy, while other studies suggest that children with more severe eczema may have lower levels of butyrate-producing bacteria—microbes that produce short-chain fatty acids which help maintain intestinal barrier integrity, support regulatory T cells and contribute to immune tolerance.
I often think about a little boy I worked with whose eczema became progressively worse over the course of a year. His parents noticed that he was reacting not only to certain foods but increasingly to pollen in the fields surrounding their home. Rather than concentrating solely on identifying the next trigger, we decided to think about what had reduced his resilience.
A comprehensive gut microbiome analysis revealed markedly reduced microbial diversity and very low levels of several bacterial species recognized for their roles in immune regulation, intestinal barrier maintenance and production of short-chain fatty acids that help regulate inflammation. The test helped us to understand why his immune system might have become less resilient and guided a more personalized approach to supporting his health.
We temporarily reduced high-histamine foods, replenished beneficial bacteria and encouraged spending more time outdoors interacting with nature. Within around eight months, he was eczema-free and remains so today.
If we focus exclusively on calming the skin while overlooking the biological systems that influence immune regulation—including the gut microbiome, intestinal barrier and microbial metabolites—we may miss opportunities to support longer-term resilience.
Eat a diverse, fiber-rich diet. Aim to eat a wide variety of different plant foods each week, such as vegetables, herbs, spices, nuts, seeds, legumes where tolerated and berries. Choose organic produce when possible.
Eat nourishing whole foods rather than highly processed, nutrient-poor ones. Make sure you’re getting enough key nutrients, especially zinc, iron and essential fatty acids, B vitamins, and vitamins A, C and D. When possible, get these from a varied, nutrient-dense diet rather than automatically reaching for supplements.
Spend time in biodiverse natural environments. Interact with nature’s microbes as much as you can by walking through forests, parks and meadows. Lie on grass, garden, plant herbs, touch plants and handle raw soil. Allow children to play outside and get dirty.
Move your body. Weave activities like walking, cycling, swimming and dancing into your everyday life. Incorporate regular strength training too.
Prioritize sleep. Aim for seven to nine hours each night. If you struggle with this, investigate natural ways to support sleep, such as using lavender aromatherapy and avoiding screen use before bedtime.
Nurture meaningful relationships. Stay connected, whether that means making time for friends and family or joining a club, class or community group.
Manage stress. There are scores of proven ways to reduce stress, from meditation and yoga to dancing and singing to getting outdoors in green spaces. Find something that works for you.
These are some foods with high levels of histamine:
Georgia Lennard, DipNT, mBANT, rCNHC, is a registered nutritional therapist and founder of That Gut Lady. She specializes in the relationship between the gut microbiome, the immune system, the brain and the skin, with a particular interest in eczema, autism and immune health. Find out more at thatgutlady.com or follow @thatgutlady on Instagram.
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