Signs Your Gut Microbiome is Unhealthy: And What You Can Do About It

Your gut microbiome is responsible for way more than just digestion. Bloating after meals, alternating constipation and diarrhea, acne and unexplained skin rashes, bad breath, and even migraines are all (potential) signs that your gut microbiome is unhealthy! The good news? There's a lot you can do about it (naturally) to bring things back into balance.

When we think about gut health, it’s easy to picture it as just the system that digests food. But your gut microbiome—the vast community of bacteria and other microorganisms living in your digestive tract—plays a much bigger role. It’s involved in everything from immune function and hormone balance to brain health and inflammation levels. A well-balanced gut supports energy, mood, skin health, and even how well you sleep.

In other words, your gut microbiome is kind of a big deal.

So what happens when things go off track? An unhealthy gut microbiome can show up in all sorts of unexpected ways. The goal of this post is to help you recognize the signs of imbalance and walk away with simple, functional steps to start restoring your gut health....no weird cleanses required, we promise.

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What is the Gut Microbiome?

The gut microbiome refers to the trillions of microorganisms—mostly bacteria, but also fungi, viruses, and other microbes—that live in your digestive tract, primarily in the large intestine. Think of it as a bustling microscopic ecosystem that plays a vital role in keeping your body running smoothly.

These microbes aren’t just passive passengers. They’re actively involved in:

• Breaking down food and extracting nutrients

• Producing vitamins like B12, folate, and vitamin K

• Training your immune system to respond appropriately

• Creating short-chain fatty acids (like butyrate) that reduce inflammation

• Preventing harmful pathogens from taking over #balance

Gut Health = Whole-Body Health

When your gut is thriving, you’re more likely to feel energized, digest food comfortably, fight off infections, and maintain a healthy weight. When your gut is out of balance (we nerds call this "dysbiosis"), it can contribute to:

• Chronic inflammation

• Autoimmune conditions

• Skin issues like eczema or acne

• Metabolic problems like insulin resistance

• Poor nutrient absorption

Key point: It’s not just about avoiding bloating (or other GI discomfort). Gut health is foundational to your entire body’s wellbeing.

The Gut–Brain Connection

Ever had a “gut feeling” or butterflies in your stomach? That’s not just a figure of speech. Your gut and brain are in constant communication via the vagus nerve and a complex system of chemical messengers—including neurotransmitters like serotonin and dopamine, which are heavily influenced by your gut microbes.

A healthy gut microbiome can help regulate mood, reduce anxiety, support focus, and promote emotional resilience. A fun fact that gets thrown around a lot, about 90% of your serotonin (your “feel good” neurotransmitter) is produced in the gut.

This gut-brain connection has illuminated the importance of taking care of your internal ecosystem. Disruptions in the microbiome (an "unhealthy gut") have been linked to depression, anxiety, brain fog, and even conditions like ADHD and Alzheimer’s.

Signs of an Unhealthy Gut Microbiome

We'll get into each category in detail, but here's the highlight reel of what's to come (click on the topic to skip ahead):

• Digestive Issues

• Unintended Weight Changes

• Sleep Trouble

• Fatigue and Low Energy

• Skin Conditions

• Autoimmune Conditions

• Mood Changes

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1. Digestive Issues

Frequent Bloating and Gas

Feeling puffy or gassy after meals on a regular basis? Occasional bloating is normal, but if it’s happening most days, your gut bacteria might be out of balance. Excess gas can be a sign that your microbes are fermenting food in ways they shouldn’t, often due to overgrowths (like SIBO) or poor digestion.

Constipation or Diarrhea

Your gut should be predictable and comfortable; not a mystery or a rollercoaster. Chronic constipation can mean your gut lacks the right balance of fiber-loving, motility-supporting microbes. On the flip side, regular diarrhea might point to inflammation, infection (parasite? pathogens?), or an irritated gut lining. Both are signs that your gut microbiome is unhealthy and is asking for support.

Food Intolerances

If you’re suddenly reacting to foods you used to handle just fine (think: bloating, cramps, or brain fog after eating), your gut could be waving a red flag. A disrupted microbiome can impair your ability to break down certain foods properly, leading to increased sensitivity or loss of oral tolerance. This often shows up with dairy, gluten, or high-FODMAP foods.

2. Unintended Weight Changes

An imbalanced microbiome can impact how your body processes food, stores fat, and regulates hunger and fullness. This is another key sign that your gut microbiome is unhealthy!

Gut Imbalance and Weight Gain

Some types of gut bacteria are better at extracting calories from food than others. When those strains dominate, you may absorb more calories from the same meals as someone with a more balanced gut. Certain bacteria also promote low-grade inflammation, which can interfere with insulin sensitivity and signal your body to store more fat (especially around the belly).

Gut Health and Unintended Weight Loss

On the flip side, if your digestion is impaired (due to inflammation, infection, or dysbiosis) you might struggle to absorb nutrients properly. That can lead to unintentional weight loss, fatigue, and even muscle wasting, especially if diarrhea or nausea are involved.

Microbes That Mess with Metabolism

Gut bacteria play a role in producing short-chain fatty acids (like butyrate), which help regulate metabolism and control appetite hormones like ghrelin and leptin. When these microbes are off, you might feel hungrier more often, crave sugar, or have a harder time feeling full.

Fun fact: this is a key mechanism behind GLP-1 agonists like Ozempic ... and supplementing with certain probiotic strains can mimic the appetite regulation effect for better weight management!

NutriDyn's UltraBiotic Akkermansia Plus is a probiotic strain that helps support weight management

A healthy gut isn’t a quick-fix weight loss plan; but it is a foundational part of long-term metabolic health.

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3. Sleep Trouble

Believe it or not, your gut and your sleep are surprisingly intertwined. In fact, your gut microbes follow their own circadian rhythm. When your microbiome is in balance, it helps regulate your internal clock, your sleep hormones, and even your overnight repair processes.

How Gut Health Supports Better Sleep

• Microbes help make melatonin: We already explained that your gut produces over 90% of your body’s serotonin. This is a key precursor to melatonin (your sleep hormone!). If your gut is off, your melatonin production can be dampened; and that means trouble falling or staying asleep.

• Anti-inflammatory balance: A healthy microbiome helps control inflammation, which is essential for deep, restorative sleep. Chronic inflammation? Cue restless nights.

Two way street: How Poor Sleep Can Worsen Gut Health

If you’re burning the candle at both ends or dealing with insomnia, your gut might start to feel the effects. Disrupted sleep can:

• Decrease microbial diversity

• Raise cortisol (which negatively impacts digestion)

• Promote sugar cravings the next day, feeding the “bad” bacteria

It's a vicious cycle: Gut dysbiosis can lead to poor sleep, Poor sleep makes dysbiosis worse. And round and round we go. If you’re constantly tossing and turning, or waking up unrefreshed despite a full night’s sleep, your gut might be the hidden culprit.

4. Fatigue and Low Energy

Chronic fatigue isn’t just about being “tired”. We define it as a deep, lingering lack of energy that doesn’t go away with rest. And while it’s easy to blame your schedule (or your coffee addiction), your gut could be the root of the problem.

Poor Absorption = Poor Fueling

Your gut is where you absorb nutrients, and if that system’s not working well, you’re not getting the raw materials your body needs to make energy. Things like iron, B12, magnesium, and CoQ10 are all crucial for energy production, and gut issues like inflammation, infections, or dysbiosis can limit their absorption.

Leaky Gut & Inflammation

When the gut lining is damaged (hello “leaky gut”), particles that should stay inside the digestive tract can sneak into the bloodstream, triggering immune responses and systemic inflammation. Chronic inflammation drains energy and leaves your body in a constant state of stress-mode.

Microbial Impact on Mitochondria

Some gut microbes produce compounds that support your mitochondria (the little energy factories in your cells or as we all learned in high school biology, "the powerhouse of the cell"). If the ratio of beneficial bugs "good bacteria" is out-of-balance with the "bad guys"—it can directly impact how well your body generates and uses energy. Yikes!!

5. Skin Conditions

Skin issues like acne, eczema, and rosacea aren’t just surface problems. They’re often signals of something deeper. Literally. The gut and the skin are closely connected through what’s known as the gut–skin axis. When the gut is inflamed or out of balance, the skin often shows it.

This can be related to impaired detoxification through the liver and gut. When this system isn't working 'up to par', your skin takes the brunt of the work.

Conditions like eczema and rosacea are often linked to an overactive or misdirected immune response. Since 70–80% of your immune system lives in the gut, any imbalance there can lead to skin hypersensitivity and persistent inflammation. We also consider fungal colonies or fungal overgrowth when issues like jock itch, athlete's foot, perioral dermatitis, or oral thrush are persistent and/or recurrent.

6. Autoimmune Conditions

Autoimmune conditions like Hashimoto’s, rheumatoid arthritis, and lupus don’t come out of nowhere. One of the biggest hidden triggers? Your gut. In fact, many autoimmune experts consider the gut to be ground zero for immune dysregulation.

When your immune system is constantly fighting off what it sees as threats leaking from the gut, it can get confused and start attacking your own tissues. This is a concept known as molecular mimicry. Over time, this chronic immune activation can flip the switch from inflammation to autoimmunity.

Research supports that leaky gut is a key step in the development of autoimmune disease, particularly in genetically predisposed individuals. [Dr. Alessio Fasano's Three Legged Stool is a great explanation for this!]

7. Mood Changes

The gut contains its own nervous system—the enteric nervous system—with over 100 million neurons. This system talks directly to your central nervous system via the vagus nerve, making the gut a major player in emotional regulation. You may be familiar with the saying, "the gut is the second brain"!

Gut Bacteria and Brain Chemistry

Anxiety, irritability, depression, and brain fog are all serious signs that your gut microbiome is unhealthy, because production of "feel good" chemicals can falter. Your microbiome produces neurotransmitters like:

• Serotonin, a happiness molecule

• GABA, which helps calm the brain

• Dopamine, involved in motivation and pleasure

When these are low, you can have mood changes even if everything else looks “normal” on paper.

Inflammation and the Mental Health Connection

An unhealthy gut often leads to low-grade inflammation, which can cross the blood-brain barrier and interfere with brain function. Studies have linked gut-driven inflammation with mood disorders like anxiety, depression, and even cognitive decline.

If your mood feels off and stress management tools aren’t helping, your gut might be what needs the reset. Supporting a healthy microbiome can be a game-changer for emotional balance and mental clarity.

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What You Can Do About It (Diet and Lifestyle Habits)

Dietary Changes

• Add Fermented Foods

  Think: sauerkraut, kimchi, kefir, yogurt (dairy-free works too), miso, and kombucha. These natural probiotic powerhouses help repopulate your gut with friendly bacteria.

• Cut the Sugar & Junk

  Excess sugar and processed foods feed harmful microbes and contribute to inflammation. Swap ultra-processed snacks for whole, colorful foods whenever you can.

• Eat More Fiber

  Your good gut bugs love fiber. Load up on fruits, veggies, legumes, nuts, and seeds to keep your microbiome well-fed and thriving.

• Consider a Gut Healing Meal Plan

  In the short term, limiting inflammatory proteins and leaky gut triggers (like gluten, dairy, + alcohol) while increasing anti-inflammatory nutrients can provide great symptom relief. For self-motivated individuals, Kate's Leaky Gut Guide is a great starting point!

  
  

Probiotics and Prebiotics

Wait... what's the difference?

• Probiotics are live beneficial bacteria (like the kind found in fermented foods or supplements).

• Prebiotics are the fibers that feed them (found in foods like garlic, onions, bananas, leeks, and oats).

  
  

Where to Get Them:

• Probiotic-rich foods: plain yogurt, tempeh, kefir, fermented veggies

• Prebiotic foods: artichokes, asparagus, green bananas, chicory root

• Supplements: Consider a high-quality probiotic with diverse strains—especially after antibiotics or during gut healing phases.

Lifestyle Modifications

• Move Your Body

  Regular movement (even walking) supports digestion, improves motility, and boosts microbial diversity.

• Manage Stress Like It Matters (Because It Does)

  Chronic stress disrupts the gut-brain axis. Try breathwork, journaling, time in nature, or even five minutes of silence to calm your system.

• Hydrate Like It’s Your Job

  Water helps move food through the digestive tract, prevents constipation, and supports microbial balance. A great goal? Aim for half your body weight in ounces per day.

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When to Call in the Pros: Microbiome Testing + More

Not Seeing Results? It Might Be Time to Test, Not Guess

If you’ve cleaned up your diet, added probiotics, and worked on stress—and your gut’s still not happy—it could be time for advanced testing. One of the best tools? The Vibrant Wellness Gut Zoomer. This comprehensive stool test looks at:

• Your gut microbiome composition

• Inflammatory markers

• Signs of leaky gut

• Pathogens, parasites, and yeast overgrowth

It's a game-changer for identifying the root cause of chronic bloating, food sensitivities, irregular bowel movements, or acne and other skin conditions. If you've got obvious signs your gut microbiome is unhealthy, this test gives you clear, actionable data.

Vibrant Wellness Gut Zoomer

Get a Personalized Gut Healing Plan

Working one-on-one with the functional medicine team at The Facility Denver means you’ll get a gut-healing plan based on your unique imbalances; not a one-size-fits-all protocol. That might include targeted antimicrobials, digestive support, dietary tweaks, or microbiome-focused supplements. Click here to explore our New Patient process.

Of course, you can always start with the Gut Zoomer and add-on a consultation with us if you need help interpreting the results!

Know When To Seek Medical Care

If you're experiencing red flag symptoms like unexplained weight loss, severe abdominal pain, persistent diarrhea, or blood in your stool: don't wait. Talk to your primary care provider or see a GI specialist right away. We work closely with specialists when advanced diagnostics are needed (colonoscopy, endoscopy, ultrasound, MRI, CT Scan, etc), but functional medicine isn't a direct replacement for this type of care!

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Microbiome Health: Final Thoughts

Your gut is more than just a digestion station—it’s a major player in your energy, mood, immune health, and even your skin. When your gut is out of balance, your body will try to tell you… and once you start listening, the path to healing becomes much clearer.

The good news? You’re not stuck with the gut you have today. Whether it’s bloating, fatigue, breakouts, or brain fog, small steps—like tweaking your diet, managing stress, or investing in stool testing like the Vibrant Wellness Gut Zoomer—can lead to big, lasting improvements.

👉 Take a moment to check in with your gut today. What’s one thing you can do to support it? Maybe it’s swapping soda for water, adding kimchi to dinner, or finally ordering that stool test.

Achieving optimal gut health can feel like a lonely road, but it doesn’t have to be. Let’s normalize the conversation—and the gas, bloating, and belly rumbles that come with it.

Your gut has a lot to say. All you have to do is listen.