Aging and hormones can have a surprising impact on your gut, says Dr Jen Pfleghaar. Here’s why it’s so important to look after your gut in midlife and what you can do to keep it healthy
I hear so often in my office, “I never had gut problems until my 40s.” Women come to me all the time saying they used to be able to eat anything they wanted, but now it makes them bloated.
They suddenly can’t tolerate wine, or they’re constipated before their period. Sometimes they’ve even developed reflux out of nowhere or they’re reacting to foods that they have never had a problem with before.
This begs the question: Why are so many women developing gut issues in midlife? It’s not that they’ve suddenly developed all these intolerances, it’s that their internal environment has changed. And this is why gut health is so important to talk about in midlife.
Think about your gut almost like a garden. The plants that grow there depend on the environment around them. Change the soil, the water, the temperature or the nutrients and you can completely change what thrives in that garden.
Your gut is similar. When hormones, stress, sleep, diet, medications and metabolism change, the environment inside the gut can change too.
The gut microbiome starts changing early in midlife, and these functional changes can set the stage for later-life health outcomes that are not optimal. Midlife is a transition period when we have hormone changes that make gut health an important area to focus on and not ignore.
This is why I don’t want women waiting until they’re 70 years old to start thinking about their gut. What’s happening in your 40s and 50s may influence how you age decades later.
Gut health is so important because the gut microbiota modulates immunity, metabolic function and even our cognitive status. There is constant communication between the organisms (bacteria) living in your gut and those in the rest of your body.
They are interacting with your immune system, producing metabolites, influencing the intestinal barrier and communicating with the brain. This is why I don’t think we can separate gut health from metabolic health, immune health or even brain health.
Some changes that happen as we age include changes in intestinal permeability and systemic inflammation. Alterations in gut barrier integrity and chronic low-grade inflammation are increasingly being studied as part of unhealthy aging.1
Did you know that gut dysbiosis, or an imbalance in the gut microbiome, may also contribute to neuroinflammation as we age? This communication is part of what we call the gut-brain axis. Current research continues to explore how the microbiome interacts with aging through both the gut-brain axis and the gut-muscle axis.2
The easiest way to understand the gut-brain axis is to picture a two-way highway. Your brain is constantly sending information down to your gut, but your gut is also sending information back up to your brain. Traffic is moving in both directions. This is one reason stress can affect your bowel movements and why changes in the gut may influence how you feel.
One change that has been studied is a reduction in Bifidobacterium and changes in the microbiome’s ability to break down carbohydrates. These changes may affect the production of short-chain fatty acids, which you can think of as important products made by beneficial gut bacteria. Changes in these microbial functions may influence inflammation and the overall gut environment.3
Your good gut bacteria make short-chain fatty acids when you feed them the right foods. They turn certain fibers that you can’t completely digest into compounds your body can use. One of these, butyrate, is an important fuel source for the cells lining the colon. This is one reason feeding the microbiome matters just as much as taking a probiotic.
Hormone levels are where gut health gets interesting for women. The estrobolome is the collection of gut bacterial genes involved in estrogen metabolism, including the ability to deconjugate (decouple from other molecules) or reactivate estrogens in the gut.
I love talking about the estrobolome because it shows women how connected our hormones and gut really are. We tend to put everything into separate boxes: Hormones go in one box, the liver goes in another, the gut goes in another. But your body doesn’t work like that. These systems are constantly talking to each other.
It gets even more complicated. Conjugated estrogens are forms of estrogen linked to other molecules, which makes them less active. They are excreted via bile into the gut, and some can be reactivated for absorption back into circulation. The activity of enzymes released by gut bacteria, such as beta-glucuronidase, can influence how much estrogen is deconjugated and potentially reabsorbed.4
An easy way to picture this is to think about the liver taking out the trash. Your liver packages estrogen metabolites and sends some of them through the bile into the intestine. Ideally, that waste keeps moving and eventually leaves through your stool. But the gut microbiome can influence whether some estrogen metabolites stay packaged for elimination or are unboxed and potentially recycled back into circulation.
Estrogen also plays a role in gut bacteria activity, gut barrier function and immune responses. The estrobolome is being studied in relation to estrogen-dependent conditions and menopausal health, although we’re still learning exactly how important these relationships are clinically.
Remember it this way: The liver metabolizes estrogen, sends metabolites into the bile, and the intestine or gut helps determine what ultimately leaves the body versus what is reabsorbed.
This is why I care so much about bowel movements when I’m talking to women about hormones. You can take every “estrogen detox” supplement available, but if you’re constipated and having a bowel movement only once every three days, we need to talk about that first.
Progesterone also has an impact on gut health. In midlife, progesterone changes and generally declines as women move toward menopause, and many women have motility changes in the gut.
They experience constipation, bloating and a feeling of being full. Since our gut and stool production are important routes for eliminating hormone metabolites, constipation is a big problem in midlife when it comes to gut health.
I know talking about bowel movements isn’t glamorous, but I ask my patients about them all the time. How often are you going? Is it easy? Do you feel like you completely emptied? Did your bowel habits change when your periods started changing? These are clues to what might be going on with their hormones.
Another problem I see in midlife is histamine.
Mast cells, which are like guards in the immune system, have estrogen receptors. Sex hormones can stimulate mast cells to make more histamine.
In the gut, there is an enzyme called diamine oxidase (DAO) that helps break down histamine that mast cells make or that we take in from food. However, estrogen can block DAO activity, leading to higher histamine levels. DAO is produced largely in the gut lining, which is another reason gut health becomes part of the histamine conversation.
Woman often tell me, “I don’t understand what happened. I used to drink a glass of wine and feel fine, and now my face flushes, my heart races, I can’t sleep or I wake up congested.” Or suddenly leftovers bother her, giving her a reaction. Or maybe her allergies are worse around certain parts of her cycle. This is when I start thinking about the entire histamine bucket rather than blaming one food group.
Think of histamine like a bucket. Your body can handle a certain amount, but different things keep adding to that bucket. Food may add some, hormonal fluctuations may add some, stress may add some and environmental exposures may add some, while gut dysfunction may reduce your ability to clear the histamine. Eventually the bucket overflows, and that’s when symptoms can become much more noticeable.
Things that can contribute to the overall histamine burden include gut dysbiosis, certain foods, environmental exposures, hormonal fluctuations, stress and impaired histamine degradation. Histamine intolerance is reported predominantly in middle-aged women, although the reasons for that pattern are not fully established in research and should not automatically be attributed to progesterone decline alone.5
What’s another thing we can control in midlife to help with gut health? Stress levels.
High stress can influence gut motility, visceral sensitivity, intestinal permeability, digestive enzyme production and the microbiome. If you focus on reducing stress or modulating it with meditation, prayer, walking outside, morning light, sleep, breathing and community, you can support your midlife gut in a positive way.
You can eat the perfect diet and take every gut supplement available, but if your nervous system thinks you’re running from a tiger all day, digestion is not going to be the body’s first priority. Gut health will suffer, and leaky gut and dysbiosis will ensue.
Midlife can be incredibly stressful. Women are raising children, helping aging parents, working, dealing with changing hormones and often sleeping poorly. It’s no wonder their digestion suddenly feels different. Your gut is listening to those stress signals and responding.
Eat real food. Start by reducing ultra-processed foods rather than obsessing over a perfect “gut diet.” It’s better to start by removing some of the things that clearly aren’t supporting the gut than to become afraid of every food.
You don’t need to wake up tomorrow and eliminate 25 foods. Start by eating food that actually looks like food and doesn’t come in a package.
Get your bowels moving. Daily movement, hydration, adequate fiber as tolerated, magnesium when appropriate and addressing why constipation exists can all be part of supporting healthy bowel function. Don’t normalize going every three or four days just because you’ve done it for years. Ask why and keep asking why until you get answers.
Feed your microbiome. Focus on a diversity of whole foods and plant fibers as tolerated rather than randomly taking dozens of probiotics. Fermented food is great for this (think kimchi, kefir and yogurt). Your microbiome needs substance also. Focus on feeding the good bacteria rather than simply throwing another probiotic capsule at the problem.
Support stomach acid. Don’t automatically assume reflux means “too much acid.” I think we are far too quick to suppress stomach acid without asking why someone suddenly developed reflux.
Stomach acid has a job, and digestion starts long before food reaches the colon. Consider bitters, try taking digestive enzymes with meals and chew your food slowly (see below).
Move. Walk after meals and strength train. Muscle and gut health may sound like two completely separate conversations, but metabolic health connects them. Walking after meals can support glucose regulation, and maintaining muscle is one of the best investments you can make in metabolic health during midlife.
Regulate your nervous system. Sleep, sunlight, prayer, breathing, community and less stimulation all matter. Sometimes supporting the gut looks like putting your phone down, going outside, praying, taking a walk and allowing your body to come out of a constant stress response.
Look at hormones. Pay attention when digestive symptoms suddenly change around the same time the menstrual cycle changes. If a 45-year-old woman tells me her gut completely changed at the same time her cycles became irregular, her sleep fell apart and she started having hot flashes, I’m not going to pretend those things are completely unrelated. Hormones are likely contributing to the gut symptoms.
Midlife is not the time to start fearing food or assuming every new symptom is something you just have to live with. It’s the time to get curious about what changed. Your gut is responding to the environment around it, including your hormones, stress, sleep, metabolism, diet and lifestyle.
Instead of chasing symptoms or endlessly restricting foods, start supporting the environment your gut needs to thrive. Feed it well, move your body, manage stress, support healthy digestion and elimination, and pay attention to your hormones.
Your gut is giving you information. Listen to it, ask why and use midlife as an opportunity to build a healthier foundation for the decades ahead.
A major component of gut health is what you put into the gut and how. Besides eating real food, there are several things you can do to help your body digest food more efficiently.
Try digestive bitters. Digestive bitters are bitter substances that work by stimulating the body to make more digestive fluids, such as saliva, stomach acid and bile, and increasing blood flow to the gut.1
Many of these are foods, such as herbs and spices: turmeric, ginger, cinnamon, citrus zest, dandelion greens, cloves and cilantro. They’re often available in supplement form as well. Others, like wormwood, burdock, aloe vera, peppermint, licorice, chamomile, coffee and artemisia are usually taken as drinks or supplements.
The best time to take bitters as supplements is 5–15 minutes before a meal, following the label instructions.
Take digestive enzymes. Changes in hormone levels that are common in perimenopause can affect the body’s production of digestive enzymes such as amylase, lactase and lipase. This can make it hard for your gut to digest some foods, which leads to bloating and discomfort.
Digestive enzyme supplements can help replace what your body no longer makes so that you can more easily break down proteins, carbohydrates or fats that now give you trouble. Consider a broad-spectrum digestive enzyme (one that helps with all these food types) with the first few bites of larger meals, following the label instructions. Adjust the dosage based on tolerance and individual need.
Before taking any supplements, it’s best to talk to your practitioner. Even herbal supplements can often have powerful effects.
Develop good eating habits. When you eat, do it mindfully. Sit at a table, chew slowly, enjoy the flavors and don’t do other activities at the same time, like watching TV or using your phone. This focus is a cue to your body that now is the time for digesting food.
Dr Jen Pfleghaar, DO, is double board-certified in emergency medicine and integrative medicine and speaks nationally on hormones, metabolic health and longevity. She is the founder of Healthy by Dr. Jen and practices root-cause medicine focused on women’s health. She lives in Tennessee on a mini farm with her husband and four children. Follow her work at @integrativedrmom and healthybydrjen.com.
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