15 Clear Signs of an Unhealthy Gut from a Trusted Functional Medicine and Hormone Doctor
What does an unhealthy gut look like?
If you’ve been feeling off lately:like your body’s misfiring and nothing seems to work the way it used to:you’re not alone. For many women in their 40s and 50s, gut symptoms creep in quietly, then start to take over: digestion goes haywire, moods swing like a pendulum, and energy becomes a distant memory.
And the kicker? Most women don’t realize their gut health might be the root cause.
That’s where functional medicine comes in. At Elle MD, we help women unravel the connection between hormonal shifts and gut dysfunction:so you can finally feel like yourself again.
In case you’re new here, we are Dr. Hendriks and Dr. Castillo MacKenzie, and we help women in perimenopause and menopause restore balance, energy, and confidence through personalized, holistic care. If your gut and hormones feel out of sync, you’re in the right place. Learn more about our
gut health services for women in Michigan.
Common Signs of Bad Gut Health
Bloating, gas, constipation, or diarrhea
Disruption in the gut microbiome can lead to poor digestion and uncomfortable symptoms like gas, bloating, irregularity, or frequent diarrhea.
IBS (Irritable Bowel Syndrome)
If you're constantly managing unpredictable digestion, cramping, or alternating constipation and diarrhea, it may point to IBS:a sign of deeper gut imbalance.
Acid reflux or heartburn
These aren’t just about stomach acid. They often stem from poor gut function or imbalanced bacteria, especially when chronic.
Persistent fatigue and poor sleep
An unhealthy gut can interfere with nutrient absorption and cortisol regulation, leaving you wired at night and exhausted by day.
Brain fog and trouble focusing
The gut-brain connection is real. Inflammation and imbalance in your gut can impair cognitive clarity, leading to mental fatigue. (Harvard Health on gut-brain connection)
Skin flare-ups (like eczema, acne, or rosacea)
Skin is a reflection of internal health. Gut dysfunction can trigger or worsen chronic skin conditions.
Mood swings, anxiety, or depression
Your gut produces neurotransmitters like serotonin. When it’s out of balance, your mood often is too.
Sugar cravings and poor appetite control
Bad bacteria feed on sugar and send signals to your brain that increase cravings, making it harder to eat balanced meals.
New or worsening food sensitivities
If you’re suddenly reacting to foods you used to tolerate, your gut lining may be compromised:known as “leaky gut.”
Unexplained weight gain or weight loss
Gut health impacts metabolism and hormone regulation. Shifts in weight with no clear cause may be microbiome-related.
Bad breath despite good hygiene
Persistent bad breath can stem from imbalances in your digestive tract or low stomach acid.
Frequent colds or infections (weakened immunity)
Your gut houses over 70% of your immune system. A disrupted microbiome can leave you more vulnerable to illness. (Cleveland Clinic on gut microbiome)
Frequent headaches or migraines
Inflammation and food sensitivities originating in the gut are common triggers for chronic headaches.
Joint pain or stiffness
Gut issues can increase systemic inflammation, which often manifests as joint discomfort.
Changes in body odor
If your body odor has changed or intensified despite good hygiene, your detox pathways:including your gut:may be overloaded.
Healthy Gut vs. Unhealthy Gut: What’s the Difference?
Your Gut as Your Second Brain
There’s a reason the gut is often called your "second brain." It houses trillions of bacteria that influence everything from digestion and metabolism to hormone production and mood.
When your gut is functioning well, it helps regulate estrogen, cortisol, thyroid function, and even neurotransmitters like serotonin. But when your gut is off? Hormones go haywire, and so does everything else.
A Healthy Gut Feels Like…
- Comfortable digestion (no bloat, no pain)
- Clear, radiant skin
- Stable energy throughout the day
- Strong immunity
- Steady moods and clear thinking
An Unhealthy Gut Feels Like…
- Constant discomfort or irregular digestion
- Breakouts or skin inflammation
- Fatigue that won’t go away
- Getting sick often
- Mood swings, irritability, or mental fog
What Causes an Unhealthy Gut?
Stress and Hormonal Imbalances
Women in perimenopause and menopause are especially vulnerable to gut issues due to fluctuating cortisol, estrogen, and progesterone levels. Chronic stress also weakens the gut lining and disrupts healthy bacteria.
Antibiotics, Medications & OTC Fixes
While sometimes necessary, antibiotics and over-the-counter medications can wipe out good bacteria, leading to long-term imbalances.
Processed Foods, Sugar, and Alcohol
These disrupt the microbiome, feed harmful bacteria, and create inflammation throughout the gut lining.
Poor Sleep and Sedentary Lifestyle
Lack of movement and restorative sleep impair gut motility and microbial diversity, compounding hormonal symptoms.
Lack of Microbial Diversity
Too much of one strain, not enough of another. A diverse microbiome is essential for resilience and hormonal balance.
Is Your Gut Trying to Get Your Attention? When to See a Functional Medicine Doctor
If you’ve cleaned up your diet and tried probiotics but still feel off, it may be time for deeper investigation. Persistent symptoms like fatigue, bloat, brain fog, or food sensitivities could indicate:
- Hormone-gut dysfunction
- Poor detoxification
- Chronic inflammation
At Elle MD, we go beyond symptom-masking with comprehensive lab testing to uncover root causes. Learn more about how our
gut health and functional medicine approach delivers personalized care.
How to Heal an Unhealthy Gut (Without Guesswork)
Start with Food:But Not Just Any Food
Support gut repair with anti-inflammatory, nutrient-dense foods:
- Fiber-rich veggies
- Fermented foods like kimchi and sauerkraut
- Bone broth
- Clean protein sources
- Hydration and mineral balance
What Is the #1 Food for Gut Health?
Fiber. Specifically, prebiotic-rich fiber found in foods like garlic, leeks, asparagus, and onions. These feed your healthy gut bacteria and promote a balanced microbiome.
Signs your gut is healing
One of the most encouraging parts of gut healing is noticing the subtle (and sometimes not-so-subtle) signs that things are improving. Physically, you may experience more regular and comfortable bowel movements, less bloating or acid reflux, and even clearer, more radiant skin. Many women also notice more consistent energy levels throughout the day and better, more restful sleep.
But gut healing isn’t just physical—it’s emotional and mental too. A balanced microbiome supports better mood regulation, so you might feel more emotionally steady, less anxious, and better able to focus. That mental fog you’ve been fighting? It starts to lift.
Healing your gut is rarely linear. But when you give your body the right tools and support, the changes are real and long-lasting—and absolutely worth the journey.
The Takeaway: Don’t Ignore the Gut-Hormone Connection
If your digestion feels off, your energy is tanking, and your mood is swinging wildly, your gut might be crying out for help. And for women in the thick of hormonal chaos, it’s not just a gut issue:it’s a full-body signal.
Don’t keep guessing. At Elle MD, we take the confusion out of healing and deliver care that’s as unique as you are.
Explore our Michigan gut health services and take the first step toward restoring balance.
Let’s create a care plan that actually works:one that supports your gut, balances your hormones, and gets you back to living fully.
Book a consultation with Elle MD today and say goodbye to the guesswork for good.
*AI Disclosure:
This content may contain sections generated with AI with the purpose of providing you with condensed helpful and relevant content, however all personal opinions are 100% human made as well as the blog post structure, outline and key takeaways.
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*Blog Disclaimer: Please note that reading our blog does not replace any health or medical advice consultation. Read our blog disclaimer here.
Meet the Drs.
Dr. Hendriks and Dr. Castillo MacKenzie are board-certified physicians, female, specialized, with over 10 years of experience.
Elle MD started after practicing in a traditional primary care setting together for over a decade. We grew frustrated with the current healthcare model, which places no emphasis on addressing the root cause of chronic disease. A lot of times, conventional care doesn’t even promote overall wellness!
We founded Elle MD in Royal Oak, MI, with a vision of providing this care in a compassionate and personalized way.
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