As a functional medicine nutritionist, I’ve reviewed hundreds of labs and seen firsthand how many health issues—especially those involving hormones—can be traced back to gut health.
The most common symptoms are weight gain despite not changing anything, fatigue, mood changes (irritability, anxiety), and lower stress tolerance…whatever they present with, there is often something going on in the gut that is causing or worsening their symptoms.
Once we address gut imbalances, inflammation, or pathogens, we may not even have to address the initial symptoms because it often resolves itself. Hippocrates was on to something hundreds of years ago!
Our gut health and hormones are more interconnected than we ever imagined, and understanding this connection not only empowers us to achieve sustainable healing and symptom relief but also live a more vibrantly healthy life for decades to come.
In this blog, we’ll explore how gut health influences hormones, the conditions and symptoms linked to gut imbalances, and the actionable steps providers can take to support their patients with testing, nutrition, and lifestyle strategies.
Table of Contents
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The Gut-Immune-Hormone Connection: Understanding Key Life Stage Shifts |
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Lab Recommendations to Assess Gut Health and Hormonal Balance |
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A disrupted gut (barrier function, dysbiosis, pathogens, digestive insufficiency) can lead to hormone imbalances that directly impact our mood, energy, stress resilience, metabolic function, and weight.
The majority of the body’s neurotransmitters are produced in the gut's lining, so gut imbalances directly influence mental health.
When discussing hormones and gut health, the conversation goes beyond sex hormones to include cortisol (stress hormones), insulin (the fat-storage hormone that regulates glucose), and satiety hormones such as GLP-1, leptin, and ghrelin. Additionally, butyrate and other short-chain fatty acids (SCFAs) work to stimulate the production of satiety hormones, which help regulate food intake and protect against diabetes by improving gut barrier function.
Many women experience gut-related symptoms like bloating and food sensitivities, especially during hormonal transitions, so it’s more important than ever to recognize and address this gut-hormone connection. By supporting gut health, we can create the conditions for hormone harmony, leading to a more energetic and healthy life.
The gut immune system impacts how our body responds to outside antigens and threats—at least 75% of the body’s immune cells are in the GI tract. This can be measured with a Gut Zoomer stool test by looking at secretory IgA (sIgA). sIgA levels are typically elevated during active immune responses, such as when the gut is exposed to pathogens, infections, or food sensitivities.
However, sIgA levels may drop when the immune system becomes fatigued or overwhelmed, such as in cases of chronic inflammation, prolonged stress, or low microbial diversity.
To gain a more comprehensive understanding of immune function, I typically add the Total Immunoglobulins panel to the Wheat Zoomer to determine how well the body is producing antibodies overall and ensure we interpret the results accurately.
Immune system function doesn’t exist in isolation—it shifts dynamically throughout a person’s life. For example, big immunological shifts often occur postpartum, followed by a profound shift in the immune system and a rise in autoimmune disease. We also see an autoimmune shift during perimenopause and menopause hormonal transitions.
These hormonal transitions bring significant challenges. Women entering perimenopause consistently complain of worsened anxiety, digestive issues, weight loss resistance, and insulin resistance. This makes sense when we consider the hormonal shifts taking place and the central role of gut health in making this transition much smoother.
By definition, menopause is an inflammatory state, as progesterone decreases and estrogen swings wildly before eventually dropping low, so addressing gut health and systemic inflammation is extremely important during this stage of life.
The interplay between gut health and hormones extends to neuroendocrine hormones, which interact with the gut via the hypothalamus, pituitary gland, and endocrine glands. These interactions directly impact sex hormones, thyroid health, and adrenal function, further illustrating the intricate relationship between the gut and the body’s broader hormonal systems.
The connection between gut health and mood is significant, as the gut plays a central role in producing key neurotransmitters that influence mental health and overall well-being. Take serotonin, our “happiness hormone,” which also promotes intestinal motility. It’s made by several strains of Lactobacillus (L.bulgaricus, L.reuteri) and requires 5-HTP and tryptophan.
Serotonin not only directly impacts mood, but locally it also promotes GI transit and colonic secretions. Low vitamin D is extremely common in my practice – it’s a hormone that impacts every cell and supports mood & neurotransmitter production. In fact, you can’t even make 5-HTP, the serotonin precursor, without sufficient vitamin D!
GABA, often referred to as our “chill hormone,” is another neurotransmitter produced by the gut. GABA is also made by several commensal gut bacteria, including Bifidobacterium, Lactobacillus, Bacteroides, Roseburia, and Akkermansia. It modulates intestinal motility and inflammation. Low GABA often indicates high stress and poor sleep, and it’s also a key player in modulating intestinal motility and inflammation.
Cortisol, the body’s primary stress hormone, also plays a critical role in gut health and hormone balance. Elevated cortisol levels can lower testosterone, growth hormone, and progesterone—hormones essential for muscle maintenance and preventing excess body fat—while raising estrogen levels.
Addressing elevated cortisol through gut health and improved sleep hygiene may not be a quick fix, but it’s a foundational step toward restoring balance and supporting long-term health.
Sleep deprivation is a significant issue—one-third of Americans fail to get the recommended seven to nine hours of sleep per night.Even mild sleep restriction can impact a range of hormones. For instance, falling short by one hour for three nights in a row leads to lower insulin sensitivity and causes a double whammy: leptin levels decrease (not feeling satiated by food), and ghrelin levels rise (hunger hormones).
In perimenopause and menopause, poor sleep is often compounded by declining levels of estrogen and progesterone, both of which contribute to sleep regulation. This hormonal imbalance further disrupts circadian rhythm and overall sleep quality, making it even more essential to address sleep as part of a comprehensive treatment plan.
Estrogen metabolism is a critical component of hormonal health, and it highlights the intersection of gut and liver function. Unconjugated estrogens are processed through the liver like toxins, so the gut health conversation has to include liver health and detoxification, as the gut microbiome helps metabolize estrogens.
The enzyme beta-glucuronidase reverses the process of glucuronidation, a Phase II detoxification reaction. When gut dysbiosis causes elevated levels of beta-glucuronidase, the enzyme can deconjugate estrogen that has been conjugated (attached) to glucuronic acid in the liver. This allows the estrogen to be reabsorbed into the bloodstream instead of excreted, effectively increasing circulating estrogen levels. Elevated estrogen levels can contribute to metabolic syndrome, PCOS, obesity, cardiovascular disease, and cancer.
Major producers of β-glucuronidase in the gut include:
Symptoms associated with elevated β-glucuronidase levels are similar to estrogen dominance, including heavy periods, clotting, cramping, fibrocystic breasts, headaches, mood swings, weight gain, fatigue, anxiety, irregular periods, infertility, and brain fog.
A Gut Zoomer stool test looks at 170 different strains of commensal bacteria, both gram-negative and gram-positive, as well as enzymes in the gut that impact estrogen. High levels of β-glucuronidase are found in an unhealthy gut and reactivate toxins and estrogens.
You can reduce it by increasing fiber intake and adding more cruciferous veggies (such as broccoli, kale, and Brussels sprouts). Cruciferous vegetables contain compounds that support estrogen detoxification pathways and promote healthier gut function.
While GLP-1 (glucagon-like peptide-1) receptor agonists are a hot topic right now, it’s important to remember that GLP-1 is naturally produced in a healthy gut. GLP-1 secretion is supported by short-chain fatty acids (SCFAs) like butyrate, which are powerhouse anti-inflammatory compounds that act as GLP-1 currency.
For this reason, it’s crucial to prioritize fiber, veggie variety, color, and polyphenols. The more fiber and color you add to the diet, the more you support the bacterial populations that produce SCFAs (aim to fill 50% of your plate with a rainbow of veggies, herbs, spices, nuts, seeds, and low glycemic fruits to feed this pathway).
Lactobacillus is important because it also has a lot of the puzzle pieces for GLP-1s, but menopause can change how thrifty the body is with hormones. One factor to consider is the Firmicutes:Bacteroidetes ratio found at the top of the Gut Zoomer (Firmicutes should be slightly smaller at around a 0.9 ratio or below).
A high Firmicutes:Bacteroidetes ratio is one contributing factor to weight loss resistance, as it indicates gut bacteria are extracting more calories from food and promoting an unhealthy metabolic profile, such as insulin resistance or small intestinal bacterial overgrowth (SIBO).
The health of the gut plays a critical role in hormonal balance, particularly through its influence on the intestinal barrier and systemic inflammation. In the GI tract, estrogen and progesterone play a positive role in tight junctions, with lower levels of these hormones contributing to thinner mucus membrane, lower diversity, and more gas, bloating, constipation, and food reactions.
When the gut barrier becomes compromised (i.e., leaky gut) and mucus-producing bacteria are insufficient, bacterial translocation increases. This means microbes can more easily cross tight junctions, activating the immune system and worsening chronic low-grade inflammation.
Increasing research shows that the gut is a major source of chronic low-grade inflammation among women, especially during hormonal transitions. Some of the best ways to support the GI tract are through stool testing, good oral health, a varied diet, prebiotics, probiotics, postbiotics (SCFAs – butyrate is looking to be very important in menopause), and anti-inflammatory foods.
Additionally, hormonal issues such as estrogen dominance have been linked to an imbalance in gut bacteria. This dysbiosis can make weight loss challenging, contribute to symptoms of PMS and menopause, and even increase the risk of hormone-related diseases. On a stool test, low diversity may look like an insufficiency of keystone bacteria or low sIgA.
When there are hormone imbalances, it’s important to understand that all hormones are made out of cholesterol—so when there is gut inflammation or sluggish gallbladder, many women begin to have trouble breaking down and emulsifying fats. Poorly absorbed fats can pass through to the colon in large globules, feeding opportunistic bacteria such as Alistipes. This further worsens gut and hormonal imbalances, creating a cycle of dysfunction.
When it comes to understanding the root causes of gut and hormone imbalances, comprehensive lab testing is
Digestive insufficiency (pancreatic enzymes, HCl, gallbladder/bile acids) is one of the most common types of dysbiosis, leading to nutrient deficiencies and worsening hormone imbalances. Combining the Gut Zoomer and the Wheat Zoomer provides rich insight into intestinal permeability as well as gut inflammation, digestive insufficiency, gluten sensitivity/Celiac spectrum and LPS (lipopolysaccharide, a neurotoxin that leads to leaky gut and blood-brain-barrier permeability).
A functional blood chemistry panel also provides important data for comprehensive gut healing and hormone balancing, including CMP, CBC with differential, lipid panel, D, B12, iron/ferritin, full thyroid panel with antibodies, A1C, insulin, leptin, and melatonin.
Improving gut health and hormonal balance requires a multifaceted approach. The following strategies outline evidence-based recommendations for nutrition, exercise, and supplementation to help optimize these interconnected systems.
Providers should recommend an unprocessed, anti-inflammatory, Mediterranean-style diet rich in polyphenols, healthy fats, and protein. Our hormones are made of cholesterol, so it’s important to consume plenty of healthy fats like olive oil, avocado, or fatty fish, but also to ensure you are breaking them down well.
The Gut Zoomer provides insights via digestive insufficiency markers, helping you determine if additional support is needed. A food-first approach to obtaining omega-3 fatty acids is ideal—fish like wild salmon, sardines, anchovies, and mackerel are the best sources. But without eating oily fish daily, it’s difficult to consume one to three grams of omega-3s every day. For this reason, I often recommend a high-quality fish oil supplement.
Beneficial bacteria like L.casei and B.breve lower B-glucuronidase activity, as does eating more plants in general. According to the American Gut Project, the healthiest people consume at least 30-50 different vibrantly colored veggies, fruits, herbs, spices, nuts, and seeds each week, so finding ways to increase variety and diversity is a great place to start. Cruciferous veggies, in particular, contain powerful compounds that support the glucuronidation pathway.
Regular exercise improves circadian rhythm and sleep, increases anti-inflammatory butyrate-producing gut bacteria, and increases microbial diversity. It helps to reset circadian rhythm, improves glucose tolerance, and increases mitochondrial function. Ideally, most people should try to get a mix of cardio and strength training.
Gut healing nutrients like L-glutamine, IgG, enzymes, bitters, probiotics, turmeric, zinc carnosine, butyrate, and omega 3s can be very helpful. If fat malabsorption or gallbladder support is needed, enzymes, betaine HCl and bitters may be used. For additional sex hormone metabolism support, calcium D-glucarate supports this pathway by inhibiting B-glucuronidase activity.
A healthy gut microbiome is critical for healthy digestion, balanced hormones, and longevity. Lab testing provides data-driven insights to impact our health for a lifetime while making informed decisions on personalized nutrition, lifestyle, and supplement interventions.
Sara Barthel is a licensed functional medicine nutritionist who helps women balance their digestion, hormones, energy, and weight naturally. She received her master's in Nutrition & Functional Medicine from the University of Western States and is a Board Certified Nutrition Specialist (CNS) and Licensed Dietitian-Nutritionist (LDN).
Sara owns a virtual practice, VibrantVia, and has worked on cutting-edge research on nutrition, gut health, and brain health. She understands the importance of an interconnected, data-driven approach and uses personalized lab testing, nutrition, and lifestyle interventions.
Sara helped create a corporate wellness program used by companies like Bayer Health and Anderson Windows. She is a former Ironman and ultramarathon athlete who is passionate about helping women achieve optimal vitality and restore balance to their bodies naturally.
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The general wellness test intended uses relate to sustaining or offering general improvement to functions associated with a general state of health while making reference to diseases or conditions. This test has been laboratory developed and its performance characteristics determined by Vibrant America LLC and Vibrant Genomics, a CLIA-certified and CAP-accredited laboratory performing the test. The lab tests referenced have not been cleared or approved by the U.S. Food and Drug Administration (FDA). Although FDA does not currently clear or approve laboratory-developed tests in the U.S., certification of the laboratory is required under CLIA to ensure the quality and validity of the test.