It wasn’t so long ago that the medical world viewed bacteria as largely infectious and dangerous. But the truth, as is so often the case, is more complex.
Bacteria can be friendly. In fact, decades of research have steadily confirmed what observant practitioners, from Hippocrates on, seemed to understand: Most disease begins in the gut. And the gut, it turns out, is governed by bacteria of all kinds.
The trillions of microbes in the gut sit at the literal center of our bodies and health, and their well-being determines more than just the quality of our digestion. The gut microbiome also influences respiratory health, mood, and hormonal balance.
“The more scientists dive into the topic, the more connections are made between gut health and pretty much every network in the body, including the neurological, cardiovascular, and immune systems,” writes integrative eco-dietitian Mary Purdy, MS, RDN, in The Microbiome Diet Reset.
Let’s examine some of the ways your gut’s microbial community contributes to your health — and how you can support your microbiome so it can keep supporting you.
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Gut Health
Most gut bacteria live in the lower part of the intestinal tract, where they help digest, absorb, and metabolize nutrients. They process fibers the body can’t digest on its own, ferment carbohydrates into short-chain fatty acids (SCFAs) that nourish colon cells, and even help produce certain vitamins, like K and B12.
They also help break down polyphenols — plant compounds found in foods like berries, tea, and dark chocolate — unlocking their anti-inflammatory and antioxidant effects.
Friendly bugs are critical for maintaining the structural integrity of the gut lining and supporting the tight junctions and mucus that prevent gut dysbiosis, which can lead to leaky gut syndrome (learn more about how a tiny leak in the delicate gut lining can cause surprisingly big problems at “How to Heal a Leaky Gut.”) These microbes feed on dietary fiber. If good bacteria go hungry due to a lack of fiber, they struggle to produce butyrate (an SCFA that reinforces the gut barrier) and may be crowded out by bugs that feed on the mucosal lining itself. This compromises the gut’s defenses.
“When the gut microbiome is disrupted, that’s when we see an increase in gut permeability, which drives systemic inflammation,” explains Minneapolis-based naturopathic doctor Sara Jean Barrett, ND.
Meanwhile, an imbalance between beneficial microbes and bacterial strains that produce methane or hydrogen has been associated with several GI disorders, including irritable bowel syndrome (IBS), Crohn’s disease, and ulcerative colitis.
Fortunately, modern interventions can often help restore the balance between helpful and harmful bugs. A 2024 review of 18 studies, published in Endocrinología, Diabetes y Nutrición, found that certain supplementary probiotics — particularly Bifidobacterium bifidum and specific multistrain combinations — may help relieve IBS symptoms such as abdominal pain and bloating in as little as four weeks (Learn more about probiotics at “Everything You Need to Know About Probiotics.”)
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Mental Wellness
Roughly 90 percent of the body’s mood-soothing serotonin is made in the gut, notes Vivian Asamoah, MD, a Houston-based integrative gastroenterologist. Other neurotransmitters, such as GABA, dopamine, and glutamate, are also synthesized by gut bacteria. That synthesis helps regulate mood, stress response, sleep, and cognitive functions like motivation and focus. (For more on GABA and mood, see “How Protein Affects Mental Health.”)
“When that process is altered by dysbiosis — whether from a postinfectious state, use of antibiotics, or diet — that will affect how those neurotransmitters are made, processed, metabolized, and passed along to the brain,” Asamoah explains.
The gut-brain connection is bidirectional, so brain signals also modify the gut.
“Emotions such as anxiety, loneliness, and depression can affect the gut microbiota as well,” she adds. An imbalanced gut microbiome may operate in a complex feedback loop with mental health challenges, each reinforcing the other.
Increasingly, functional practitioners are taking a multidisciplinary approach to untangling these loops. Asamoah often recommends that her patients work on diet and lifestyle changes to support the microbiome while partnering with a GI psychologist to help with stress reduction and emotional regulation.
Research shows that a type of bacteria known as psychobiotics can also be particularly supportive. “Certain strains of Bifidobacterium, Lactobacillus, and Akkermansia play key roles in gut-brain health,” she says. “We often see low levels of Akkermansia in patients with gut-brain axis issues, so we focus on restoring it, often by increasing polyphenols in the diet that help support its growth.”
Several studies indicate that Akkermansia supplementation can improve depression-like symptoms in mice. And a randomized controlled trial published in Translational Psychiatry in 2022 found that a short-term, high-dose, multistrain probiotic significantly reduced depression symptoms in people with major depressive disorder; the probiotic boosted levels of Lactobacillus in the gut and even changed patterns of brain activity. (Learn more at “Psychobiotics: Using Gut Bacteria to Treat Mental Illness.”)
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Skin Health
It may not surprise you that inflammation in the gut can show up on the skin as acne, eczema, or rosacea, but new research suggests that skin health may also influence the gut.
“We’ve always thought in functional medicine that disruptions in the gut microbiome can lead to skin concerns,” Barrett says. “But now we’re learning that damage to the skin barrier can actually cause changes to the gut microbiome as well.” A study of mice, published in Nature Communications in 2024, found that wounded skin can alter the microbiome and immune activity in the colon.
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Cognitive Function
The gut-brain axis not only influences how we feel day to day: It may also affect how our brains age and function over time, even playing a role in our risk for neurodegenerative diseases such as Alzheimer’s and Parkinson’s.
One of the most important ways the gut influences cognitive health is through its effect on the blood-brain barrier, which protects the brain and spinal cord from harmful substances. Recent research shows that gut microbes play a surprising role in keeping the barrier strong and selective.
When researchers compared germ-free mice and mice with healthy gut bacteria, the germ-free mice had increased blood-brain barrier permeability. But when they received either a fecal transplant from healthy mice or supplements of SCFA-producing bacteria, the integrity was restored.
When the blood-brain barrier is leaky, harmful molecules and immune cells can cross into the brain and trigger neuroinflammation. And a lack of gut microbes that produce key metabolites can affect the behavior of microglial cells — the immunity defense in the central nervous system — leading to excessive synaptic pruning and damage to healthy brain tissue.
Studies show that people with Alzheimer’s disease tend to have gut bacterial compositions that differ from healthy individuals, often including a higher proportion of the proinflammatory Collinsella strain.
Researchers are increasingly looking at whether manipulating the microbiome with diet or probiotic supplements can reduce the risk or affect the progression of neurodegenerative diseases. A 2024 systematic review in the International Journal of General Medicine found that probiotics show promise in helping treat symptoms of Alzheimer’s, Parkinson’s, and multiple sclerosis.
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Immune Response
Gut microbes play a huge role in determining how well the immune system operates. “Seventy to 80 percent of our immune tissue is located in or around our GI tract, which means that our gut microbes are constantly communicating with our immune system,” Barrett says.
Gut dysbiosis is recognized more as a driver of systemic autoimmune diseases, such as type 1 diabetes and rheumatoid arthritis (RA). Researchers have identified specific microbes that create SCFAs that educate regulatory T cells and promote the production of anti-inflammatory cytokines to help maintain immune balance.
Other microbes, when they overgrow, have been linked to inflammation and immune dysregulation. Patients with RA, for instance, tend to harbor low levels of helpful Faecalibacterium and an overabundance of the inflammation-fueling Prevotella species.
The key to a strong immune system is sufficient bacterial diversity. “[A well-populated] microbiome promotes a healthy balance between the T-regulatory cells and inflammatory T cells,” Barrett says. “It really plays a critical role in helping to protect you from autoimmune diseases.”
This understanding of the gut-immune axis may lead to new strategies for cancer prevention and treatment. Already, scientists have found that certain gut bacteria, such as Akkermansia muciniphila, can boost the effects of cancer immunotherapy by helping immune cells target tumors more effectively.
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Cardiometabolic Health
Humans and our gut bugs are sometimes described by researchers as “metabolically active superorganism[s].” Studies have found that microbes play key roles in weight gain, metabolic obesity, and general metabolic health, including in blood-sugar and cholesterol management.
For example, a shortage of butyrate-producing bacteria, mainly from the Firmicutes group, has been linked to type 2 diabetes and obesity. Conversely, beneficial microbes help build butyrate, which can regulate appetite and enhance insulin sensitivity.
Dysbiosis has also been linked to cardiovascular risk factors, such as atherosclerosis, hypertension, heart failure, and chronic kidney disease.
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Allergic Sensitivities
In recent years, researchers have connected rising allergy rates in children to declining microbial diversity. Babies born via C-section, fed formula, or exposed to antibiotics early in life tend to have different gut bugs than those delivered vaginally, breastfed, or raised with regular exposure to dirt, animals, and other kids.
“It’s really the early microbial exposures that set the immune tone for allergies,” Barrett says.
This idea is the central tenet of the hygiene hypothesis, which posits that modern life is a little too sterile: Without regular encounters with microbes, the immune system doesn’t get the stimulation it needs to mature properly. (Learn why a little exposure to germs and viruses is good for your health at “Why Some Germs Are Good for Immunity.”)
A similar theory, the “old friends” hypothesis, suggests that humans evolved in regular contact with certain microbes from soil, animals, and other people. When we lose those “old friends,” the immune system can misfire.
Some encouraging studies suggest that restoring beneficial bugs through diet, outdoor exposure, or even specific probiotics may help reduce the risk of developing allergies, especially early in life.
A study published in Science Advances in 2020 compared the gut microbiomes of children who spent four weeks playing in standard urban daycare centers with those of children who played in daycares with more green space. The exposure to green space corresponded to greater microbial diversity and other improvements in immune health.
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Respiratory Wellness
As with allergies, your body’s ability to fend off mild or serious respiratory conditions, such as colds, flu, asthma, or pneumonia, is partly determined by your gut health.
“Microbial metabolites [like SCFAs] and immune signaling affect airway inflammation and your susceptibility to respiratory infection,” Barrett says, adding that these communications happen through the gut-lung axis.
Studies show that certain respiratory conditions — specifically chronic obstructive pulmonary disease (COPD), asthma, and lung cancer — often go hand in hand with gut dysbiosis. Children with asthma tend to host lower levels of beneficial Bifidobacteria and Lactobacilli bacteria and higher levels of Proteobacteria and Firmicutes than children without asthma. And people with lung cancer may have lower levels of some bacterial strains that counter inflammation.
Like the gut-brain axis, the gut-lung axis is bidirectional. Respiratory infections such as COVID-19 can lead to gut dysbiosis, and, according to animal studies, respiratory infections in general can cause a decrease in beneficial gut bacteria.
More positively, abundant SCFAs in the gut are linked to lower levels of lung inflammation, protection against COPD, and, in kids, a lower risk for asthma. A placebo-controlled study of 40 asthmatic adults published in Allergy, Asthma & Clinical Immunology in 2023 found that eight weeks of supplementation with a probiotic led to significant improvements in lung function.
(Our lungs are essential to life — and our immunity. Learn what you can do to support them in the face of increasing air pollution — plus, lung-healing foods — at “Take a Deep Breath: Understanding Lung Health and Immunity.”)
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Hormonal Balance
Hormones and the microbiome also have a bidirectional relationship. Gut bugs help metabolize and recycle hormones, such as estrogen and testosterone, and hormones can make direct changes to the microbiome.
Well-balanced hormones and gut microbes help regulate mood, metabolism, menstrual cycles, and immune function. But when either is disrupted by stress, illness, medication, or diet, both systems can be thrown off at the same time.
A disrupted microbiome can lead to constipation, for example, which can reduce the body’s ability to clear excess estrogen. This increases the risk of hormone-sensitive conditions like endometriosis and breast cancer.
And hormonal shifts during puberty, pregnancy, and menopause can reshape the gut microbiome, sometimes leading to changes in gut permeability, inflammation, or metabolism.
Support Your Microbiome
Each of us has a gut microbiome that’s as unique as our fingerprints. “The bacteria hanging out in your gut might be quite unlike those spending time in your best friend’s gut because of the differences in your backgrounds, lifestyle, genetics, and food consumption,” Purdy writes.
There’s no universal model for an ideal microbiome, but healthy gut communities typically have the following characteristics:
- Diversity, or a wide variety of microbial species
- Richness, or a high overall number of microbes
- Stability, or the ability to maintain balance over time, even after illness, stress, or antibiotics
- Beneficial function, including through strong production of SCFAs like butyrate, balanced immune signaling, and support for the gut lining
- Low levels of inflammation, signaled by fewer markers of gut irritation or immune overactivation
Daily habits go a long way in supporting these qualities. “We can see radical change in people’s microbiomes and how they’re feeling within a few weeks to months of focusing on the basics of optimizing gut health,” says Asamoah.
Help optimize your own gut with these behaviors.
1. Focus on fiber. Certain bacteria turn the indigestible fibers and starches in food into lactic acid, which supports digestion. These starches and fibers, called prebiotics, act as fuel for healthy gut bugs. Barrett notes that cooking rice or potatoes and refrigerating them for at least 24 hours increases their resistant starch content. Reheating doesn’t destroy it, so enjoy them hot or cold.
2. Eat the rainbow. Colorful plant foods are rich in compounds called polyphenols, which act like fertilizer for beneficial gut microbes. Berries, leafy greens, purple cabbage, turmeric, and other vividly colored produce and spices offer antioxidants and microbiome-friendly fuel.
Variety is key: The more types of plants you eat, the more diverse your microbiome becomes, because different bugs thrive on different polyphenols. For instance, a beneficial strain of Akkermansia, which protects the gut lining, loves to feast on the polyphenols in pomegranates and red apple skins.
3. Enjoy fermented foods. You can feed good gut bugs only if they’re there in the first place, so why not add some to the mix? This is where fermented foods and drinks like yogurt, kefir, sauerkraut, kimchi, miso, and kombucha come in. They’re full of friendly microbes that help reinforce the gut barrier, counter inflammation, and bolster immunity. Daily intake of fermented foods has been shown to reduce inflammation and increase beneficial gut bacteria. (Check out “9 Benefits of Eating Fermented Foods” for more.)
4. Exercise. Studies show that people who exercise consistently tend to have more beneficial bacteria, including those that produce anti-inflammatory compounds like SCFAs. Even moderate movement, like brisk walking, yoga, or cycling, can support the microbiome.
5. Get outside. Being in nature increases your contact with a range of environmental microbes, which may help diversify your microbiome. Gardening, hiking in nature, and interacting with animals can all support this microbial cross-training. Even rubbing soil and plant material on your hands may increase microbial diversity in the gut and skin, at least temporarily.
6. Manage stress. The gut and brain are in constant communication through the gut-brain axis. Chronic stress can affect this communication, altering microbial balance, increasing inflammation, and impairing digestion.
Practices like breathing deeply, meditating, and improving sleep hygiene may help reduce stress and support a healthier gut. In turn, a well-balanced gut can improve mood, lower anxiety, and help regulate the body’s stress response.
7. Choose nontoxic cleaning products. Excessive use of antibacterial products can disrupt your body’s friendly bacteria. “I personally don’t like hand sanitizer, because [its] ingredients can disrupt the balance of the skin microbiome,” Barrett says. “They don’t discriminate and can end up killing off the beneficial organisms along with the harmful ones.” (Many popular household cleaners are dangerously toxic. Learn about the eight scariest substances at “8 Hidden Toxins Lurking in Your Cleaning Products,.“)
Opt for simpler, nontoxic cleaning products for your home and body when possible. Save stronger disinfectants for when you really need them. (Learn how to make your own at “Make Your Own Cleaning Products With These 4 Recipes.”)
8. Use probiotics as needed. Probiotic supplements can be helpful in certain situations — particularly during or after a round of antibiotics or as part of a gut-healing program.
“Incorporating more fermented foods and prebiotics into your diet enriches the microbiome in a more natural way,” Asamoah says. “But I also prescribe probiotic supplements in specific cases, like chronic constipation or antibiotic-associated diarrhea. In most cases, I don’t recommend staying on a probiotic for longer than about three months without reevaluating your needs.”
Purdy agrees. “Which diseases, which effects, which probiotic species, how much, and for whom are still very much being explored,” she notes. “Probiotic supplements . . . can help digestive function but may offer very little benefit if diet and lifestyle habits aren’t also shifting in a more supportive direction.”
In short, aim for diversity in all things: A fiber-rich and colorful diet, time outdoors, stress management, and regular exercise all go a long way in creating a more resilient gut — and a healthier you. Focus on fiber. Certain bacteria turn the indigestible fibers and starches in food into lactic acid, which supports digestion. These starches and fibers, called prebiotics, act as fuel for healthy gut bugs. Barrett notes that cooking rice or potatoes and refrigerating them for at least 24 hours increases their resistant starch content. Reheating doesn’t destroy it, so enjoy them hot or cold.
This article originally appeared as “The Mighty Microbiome” in the March/April 2026 issue of Experience Life.
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