10: Why Your Gut Went Rogue in Perimenopause (Part 1)

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Why Your Gut Went Rogue in Perimenopause

The Wake-Up Call

If you’re dealing with bloating that makes you look six months pregnant by dinner, brain fog that has you forgetting words mid-sentence, or cravings so intense you’d fight someone for their sandwich, your gut might be screaming for help. And in perimenopause your gut needs some extra love because dropping estrogen is changing everything down there.

Microbiome 101: The Basics

Let’s start with the basics. You have a nice long tube from your mouth to your anus, and this is like a really big straw in the middle of your body. It lets food and nutrients in and keeps viruses, bacteria, and other pathogens out. The majority of your immune system is in your gut. Anything that you put in your mouth has to go through your gut first, so it makes sense to have so much of your immune system there.

Inside of your gut are a bunch of tiny little friends that digest foods that you can’t like insoluble fiber and make some important things that you can’t, like short chain fatty acids and vitamin K. They also create bulk to form your stools and play a role in motility. If it’s too fast, you get loose bowel movements, and if it’s too slow, you experience constipation. Neither is fun.

The little friends in your gut are bacteria, viruses, yeast, and fungi. We actually have populations of these friends all over our bodies – on your skin, in your eyes, in your nose, and in your vagina.

So all of these things start to grow in your gut, which starts to be populated after you’re born from your mom’s microbiome and breast milk. We don’t know a lot about all of the jobs these friends have, but we do know they are necessary for humans to live and that fiber is an important food source for them.

We also know that there are groups of people who eat very little fiber and are able to thrive with very little chronic disease, but we don’t know if they have a different set of microbes passed down from generation to generation to support that type of diet or if there’s some other factor keeping them healthy. This is something that we noticed amongst populations who’ve not been influenced as much by Western culture and diets.

Fiber: Not as Hard as You Think

Generally speaking, better gut health is related to higher fiber consumption and a variety of fibers in plants. You can modulate the gut with powder fibers but would need quite a lot to consume the amount of fiber with powder that you would need to reach your daily recommendations, which is 25 grams of fiber for a female.

To give you some context around foods:

• One cup of broccoli has 5 grams of fiber
• One cup of raspberries has 8 grams of fiber
• One cup of canned black beans has 18 grams of fiber

So if you have one cup of black beans and one cup of raspberries, you’re already at 26 grams of fiber. Total win. So it’s not as crazy hard as it sounds to hit those fiber goals. If you have some veggies during the day, you’re probably getting over 30.

What Changes Your Microbiome?

Okay, now we know what the microbiome is made of and what it’s eating. So what causes changes in the microbiome?

• Nutrition
• Antibiotic usage
• Stress
• Sleep disruption and circadian rhythm disruptions
• For women, times of hormonal shifts like puberty, pregnancy, and perimenopause

We know that a week of travel can completely change your microbiome. We also know that your microbiome can change your cravings, your metabolism, and disrupt your sleep.

The Perimenopause Plot Twist

And here’s where perimenopause gets really interesting, and honestly, can be very frustrating. If you’ve suddenly developed gut issues in your 40s that you never had before, you’re not imagining it. Your gut microbiome is actually changing because of your hormones.

Let me explain how this happens. Estrogen and progesterone don’t just affect your periods and hot flashes. They’re actively involved in managing your gut. Estrogen influences how fast food moves through your digestive tract, which is why some women suddenly become constipated in perimenopause while others are running to the bathroom.

These hormones also help maintain the diversity of your microbiome. Basically, they help to keep a good variety of bacteria hanging around. And they play a role in something called the estrobolome which is a collection of bacteria that help metabolize and recycle estrogen. When your estrogen starts dropping and fluctuating wildly in perimenopause, this whole system gets disrupted.

What This Actually Looks Like

So what does this actually look like? You might notice:

• Bloating that seems to come out of nowhere, especially in the second half of your cycle
• Food sensitivities you never had before – suddenly dairy doesn’t agree with you or gluten makes you feel like garbage
• Unpredictable digestion – constipated one week, loose stools the next
• More inflammation throughout your body, which shows up as joint pain, skin issues, or just feeling puffy
• Metabolism changes – the same gut that used to efficiently process your food is now contributing to insulin resistance and weight gain, especially around the middle

The Vaginal Microbiome Connection

The vaginal microbiome is going through changes too, and we need to talk about this because not many people are. Your vagina has its own ecosystem of bacteria, primarily lactobacilli, and that keeps the pH acidic to protect against infections. Estrogen supports these lactobacilli, so as estrogen drops in perimenopause, the vaginal microbiome becomes less diverse and less protective.

This is why UTIs, yeast infections, and bacterial vaginosis suddenly become more common in your 40s and 50s, even if you’ve never dealt with them before. It’s not poor hygiene, and it’s not that you’re doing something wrong. It’s perimenopause changing your microbiome.

And here’s something that will really blow your mind. Your gut microbiome and your vaginal microbiome talk to each other. They’re connected through something called the gut-vagina axis. So when your gut is struggling, it can make vaginal issues worse. And when you’re dealing with recurring vaginal infections, it can affect your gut. They’re in this together.

Quick pause: If you’re sitting here thinking, “Oh my god, this is exactly what I’m experiencing,” would you share this episode with one friend going through perimenopause? Screenshot it and send it her way and tell her “this explains so much,” because I guarantee she’s dealing with some version of this too, and her doctor probably told her it’s normal aging. Let’s change that narrative together.

This is also why probiotics marketed for women’s health often contain lactobacillus strains. They’re trying to support both ecosystems. And it’s why when we talk about gut health in perimenopause, we’re not just talking about bloating and digestion. We’re talking about UTIs, vaginal dryness, recurring infections, and overall resilience.

The Nuance of “Good” vs “Bad” Bacteria

Now, I know we all like to categorize things as good or bad, healthy or not healthy, but like many things, there’s a lot of gray area – which is to say, nuance. We can’t really think of bacteria as inherently good or bad. It’s more about the ecosystem and real estate.

Healthy microbiomes do have some of the “bad” bacteria like C. diff and E. coli. It seems like they are part of a natural ecosystem. The problems arise when they get too much real estate.

Conditions Connected to Gut Health

What are some things commonly associated with gut and microbiome issues?

• Autoimmune diseases and autoimmune processes
• Skin disruptions like psoriasis, eczema, rosacea, rashes, and breakouts
• Fatigue, sleep, and circadian rhythm disruptions
• GI symptoms like gas, bloating, constipation, loose bowel movements, abdominal distension, proton pump inhibitor usage
• Mood changes, depression, anxiety
• Hormones and endocrine issues because of disruptions to the estrobolome
• Metabolic health and metabolism
• Allergies and asthma
• Non-alcoholic fatty liver disease, diabetic kidney disease and NASH
• Cardiovascular disease

That’s a lot of things! I think it’s important to remember that many conditions are connected to the gut directly or indirectly, and the connection often goes both ways, meaning the condition can influence gut issues and gut issues can influence the condition.

Hippocrates, of the Hippocratic Oath to do no harm, is often credited with the phrase “all disease begins in the gut.” Now, not all disease begins in the gut, but it’s connected to quite a long list.

How Gut Issues Worsen Perimenopause Symptoms

And in perimenopause specifically, you might notice the gut issues seem to make your hormonal symptoms worse. Poor gut health can increase inflammation, which can worsen hot flashes and night sweats.

It can affect your serotonin production. About 90% of your body’s serotonin is produced in your gut. And while that gut serotonin doesn’t directly cross into your brain, your gut microbiome influences your brain’s serotonin production through the gut-brain axis. A struggling gut can affect mood, sleep, and how you experience pain.

A struggling gut can also make insulin resistance worse, leading to more weight gain and energy crashes. So when we heal the gut, we’re often improving multiple perimenopause symptoms at once.

Stop Over-Sanitizing Everything

So, you want a healthier gut, what do we do? One of the mistakes I see happening a lot is this desire to disinfect everything. I know this is alluring. We all learned about germ theory and Louis Pasteur, and so it always seems like more is better.

You definitely want your surgeon, dentist, and gynecologist disinfecting their hands, killing as much of the bacteria as possible. But you, my sweet peri-friend, do not want to disinfect. You do not want to kill 99% of all germs in your mouth, on your hands, or in your body.

The bacteria, viruses, yeast, and fungi in and around us are mostly our friends. They live in a beautiful, mutually beneficial relationship with us. So we want to tend to them and take care of them because we need them to live.

Are there bad actors? Absolutely. Are there bacteria and infections that cause problems for us and get us sick? Yeah, you bet. But we don’t want to be continuously carpet bombing our different biomes and disrupting the ecosystems that are there to protect us.

Things that can cause disruption to our different biomes:

• Alcohol-based mouthwashes
• Hand sanitizers
• Disinfectant sprays and cleaning materials
• Unnecessary antibiotics
• Douching and other vaginal cleansers
• Chemical-based period and sexual health products
• Makeup and body products with endocrine disruptors
• Any product that talks about its ability to kill off lots of bacteria, viruses, and microbes

Oral Health is Gut Health

Good gut health starts in the mouth. So your oral health is really important here. Your mouth is constantly seeding your gut through swallowing food, but also saliva, bacteria, and anything produced in the mouth, good or bad.

If you have an inflamed, infected, or diseased mouth, it will cause downstream effects in the gut and can lead to gut issues like bloating and fatigue. Inversely, poor gut health like dysbiosis and leaky gut can cause issues with digestion and absorption, which can lead to low levels of nutrients necessary to remineralize your teeth. If your teeth can’t remineralize, then you end up with cavities.

There’s an entire ecosystem of little friends that are helping to start breaking down food, protect your mouth against unfriendly bacteria and viruses, and manage the pH of your mouth, helping with repairs. We want to keep our mouth ecosystem healthy by brushing and flossing every day.

The Xylitol Solution

Consider a xylitol mouthwash. I will link to the homemade recipe that I use, but you can also find brands that make it. Xylitol is a sweetener, a sugar alcohol, that has really great effects on oral health, specifically preventing biofilms from growing (which are like little protection bubbles around bacteria) and preventing the growth of some pathogenic bacteria.

In kids, it’s useful in decreasing the amount of cavities, but it’s not as effective in adults.

Alcohol-based mouthwashes that disinfect – meaning they kill the majority of our little friends – are not helpful and they are damaging. They kill all of the organisms in your mouth, friendly or not, which leaves a lot of open real estate for opportunistic bacteria to move in.

You can use salt water with a few drops of peppermint oil if you want a minty-fresh feeling and don’t feel like using a xylitol mouthwash.

Gum Health in Perimenopause

I also want to mention gum health specifically because it becomes more important in perimenopause. Dropping estrogen can cause more gum inflammation and periodontal issues. And here’s the connection: The bacteria from inflamed gums can travel through your bloodstream and contribute to systemic inflammation, insulin resistance, and cardiovascular disease.

So that twice-yearly dental cleaning? Not an option anymore. If your dentist mentions gum inflammation or recession, take it very seriously. This is another way that perimenopause is making gut health and oral health more critical.

Coming Next Week

So next week, we’re diving into the practical stuff. What should you actually eat? What about fermented foods and probiotics? I’m going to walk you through my exact protocol for protecting your gut when you need antibiotics, give you the 40 plant food framework that makes increasing variety actually doable, and tell you when it’s time to call in practitioner support versus when you can DIY this.

Because understanding what’s happening is step one, but you need the practical tools to actually support your gut through perimenopause.

Your gut isn’t broken, your perimenopause isn’t in your head, and next week you’ll have a clear action plan. See you then.