5 Signs Your Microbiome Needs Support

From brain fog to bloating, here’s how your microbiome may be calling for help.

About a decade ago, I was living what most would call a dream life, traveling the world, competing as a high-level triathlete, and working in New York’s fast-paced fashion industry. I thrived on momentum and performance. But then, my body hit the brakes. Hard.

What began as a mild fatigue and intermittent GI discomfort spiraled into full-body exhaustion. Walking up a flight of stairs felt like a marathon. Brain fog, strange rashes, unexplained joint pain, rapid weight loss, and a storm of gut symptoms soon followed.

I saw doctor after doctor, GI specialists, neurologists, oncologists, even psychiatrists. I was tested for everything from autoimmune disorders to tropical diseases to cancer. The results? Inconclusive. The treatments? A long list of prescriptions that didn’t address the root cause and only addressed my symptoms.  At one point I was told it was “all in my head,” then a week later, I was told I might have cancer. I was bounced between extremes, without answers or a plan.

At my lowest point, I was physically wrecked, mentally fogged, and emotionally shattered. I didn’t recognize the person in the mirror. I had lost over 40 lbs, my eyes were dark and sunken and I’d lost the joy to live. 

The turning point came about a year and a half into this struggle when I met a functional medicine doctor who asked a question no one else had:

“Have you looked into your gut health?”

That single question changed everything. With further testing, we discovered severe dysbiosis, parasites, and elevated inflammation. Finally, I had a direction and something I could sink my teeth into. But more importantly I had a renewed sense of hope.

The process of healing and supporting my gut and microbiome didn’t just improve my symptoms over time, it helped me rebuild my sense of self. My clarity, energy, and confidence slowly returned. Week by week, month by month I began to feel like myself again.

Why Your Microbiome is Essential for Longevity

Your gut is home to trillions of bacteria, fungi, and viruses, collectively known as your microbiome. This inner ecosystem regulates everything from digestion and immunity to mood, memory, and inflammation. It even communicates with your brain through the vagus nerve and produces neurotransmitters like serotonin and dopamine.

When your microbiome is in balance, you feel grounded, focused, and energized. But when it’s disrupted by stress, antibiotics, processed food, or environmental toxins, your health can unravel.

I didn’t understand this at the time, but years of stress, overtraining, overuse of antibiotics, and a diet I thought was healthy had quietly eroded my gut health. That imbalance set the stage for deeper issues, including chronic Lyme infection that my immune system could no longer keep in check. It was only when my gut began to heal and build a more resilient microbiome that my body was able to fight off chronic infections and eliminate all the toxic buildup that had accumulated over the years. I needed a full body reset, which is possible when you give your body the proper nutrients, manage stress, and get back into alignment with the natural rhythm our bodies are designed for.

5 Signs Your Microbiome Needs Support

When I was deep in my own healing journey, I remember the frustration of doing everything right, eating clean, exercising, trying every supplement under the sun, and still feeling terrible. That was the wake-up call: it wasn’t just about what I was doing. It was about what my body could actually absorb, process, and handle. And that all comes back to gut health.

Here are some common signs your microbiome might be out of balance and why that  matters:

1) Chronic Bloating, Gas, or Constipation

These aren’t just annoying digestive issues, they’re signals that your microbiome might be imbalanced or inflamed. A lack of diverse, beneficial bacteria can impair digestion, slow motility, and cause fermentation in the gut (hello, gas and bloating). Studies show that dysbiosis (a disruption in gut flora) is commonly linked to irritable bowel symptoms and altered motility patterns in the colon.

2) Growing Food Sensitivities

If it seems like you’re suddenly reacting to foods you used to tolerate like dairy, eggs, nightshades, even certain vegetables it may be due to increased intestinal permeability, often called “leaky gut.” When the gut lining is compromised, undigested particles and toxins can slip through and trigger immune reactions. Research has shown that gut barrier dysfunction plays a key role in food sensitivities and the development of autoimmune diseases. 

3) Skin Breakouts, Rashes, or Eczema

Your skin is often a reflection of what’s happening internally. Gut inflammation and microbial imbalances can lead to skin conditions like eczema, psoriasis, and acne. This gut–skin axis is well documented. A 2018 study highlighted the link between gut dysbiosis and inflammatory skin conditions, showing that improving gut health can lead to significant skin improvements. 

4) Brain Fog, Fatigue, or Low Mood

The gut and brain are in constant communication via the vagus nerve and a network of neurochemical messengers. When your gut is inflamed or out of balance, it can create problems with neurotransmitters like serotonin and GABA, which help regulate mood, focus, and sleep. Studies show that people with gut dysbiosis often have higher rates of anxiety, depression, and cognitive dysfunction.

5) Autoimmune Symptoms or Frequent Illness

Your gut houses over 70% to 80% of your immune cells. When the microbiome is imbalanced, the immune system can go into overdrive, attacking your own tissues or becoming overly sensitive to environmental triggers. A 2024 review in Frontiers in Immunology linked microbiome disruption to the onset of autoimmune diseases, from rheumatoid arthritis to lupus.

If you have experienced or struggled with any of these symptoms, that could be a sign your body is trying to communicate with you to take action. 

A 4-Step Guide to Restoring Gut Health and Reclaiming Your Energy

This is the same framework I now use with clients who are navigating midlife health challenges, from fatigue and brain fog to autoimmunity and weight gain. It’s simple, science-backed, and sustainable over time. 

1. Start with a Vision

Healing isn’t just about symptom relief; it’s about reconnecting with who you are and the life you want to live.

That’s why I ask clients a few key questions right out of the gate:

• What does better health make possible for you?
  Maybe it’s traveling again, playing with your grandkids, or simply waking up with energy and purpose. This question helps you shift from symptom-chasing to purpose-driven healing.
  
• What would it feel like to have energy again?
  Imagining it helps your brain create new pathways. As Stanford researcher Dr. BJ Fogg teaches, behavior change sticks when it’s anchored in emotional meaning, not just willpower, which is a fleeting emotion.
  
• What would you do if you trusted your body again?
  Illness often erodes trust in our bodies. But you’re not broken. Your body’s been doing its best to adapt. Rebuilding trust is a key part of healing.
  

These questions are your compass. They help rewire your brain and keep you focused when motivation dips.

One of my favorite sayings is “Let go of perfection. Focus on the direction.” That’s how we get there, step by step, day by day.

2. Simplify What You Eat

You don’t need a complex elimination diet to start. You just need consistency and nourishment.

• Focus on whole, real foods with minimal ingredients
  
• Cut down sugar, processed grains, refined oils, and dairy (if sensitive)
  
• Eat anti-inflammatory, gut-friendly staples like: bone broth, wild fish, leafy greens, fermented veggies, and healthy fats. HERE is a Food Dictionary to help highlight foods to enjoy and ones to avoid to keep your microbiome healthy.
  
• Avoid extremes, your body craves rhythm, not restriction.

The goal is to nourish your microbiome with the foods it recognizes and thrives on, nutrients that are familiar to your biology and aligned with how humans have evolved to eat for millennia. These healing foods are powerful because they work with your body, not against it. Remember, food is the input we give our bodies multiple times a day. It fuels every cell, drives every function, and influences how we feel. That’s why cultivating awareness around what you eat is so important, because it’s one of the few things you have full control over

3. Try This Body Scan to Listen to Your Body

In a world obsessed with tracking and tech, we’ve lost touch with our most powerful biofeedback system, ourselves.

• Pay attention to how food, stress, and sleep affect your body
  
• Notice how your digestion feels after meals
  
• Reflect on your energy, mood, and clarity throughout the day.
  

Daily check-ins are more valuable than any app or metric. Tuning into your own signals is the foundation of intuitive health.

Need help connecting with your body again? Here is Body Scan Meditation that helps deepen the mind/body connection and brings more awareness to the sensations in your body. 

4. Get Support (and Give Yourself Grace)

You don’t have to do this alone. In fact, you’re not meant to.

Creating real, sustained change requires more than just willpower or information, it requires connection. A strong support system can help carry you through the hard days and celebrate the small wins along the way. These four pillars form the foundation of a support system that truly nourishes your healing journey:

• Partnership – Co-create Your Path
  True transformation happens in partnership—not through top-down instruction, but through collaboration. A good support system doesn’t dictate your direction; it walks beside you. Whether it’s a coach, a close friend, or a trusted community, choose partners who respect your agency and support your vision, while offering perspective, tools, and encouragement as you navigate your path forward.
• Acceptance – Start Where You Are
  Real change begins with radical acceptance. That means acknowledging your current reality—your symptoms, your struggles, your story—without judgment. Healing doesn’t require you to be anywhere other than where you are right now. Acceptance creates the foundation for sustainable progress by freeing you from shame, comparison, and perfectionism. It’s the compassionate lens through which real, meaningful change can begin.
• Compassion – Embrace the Journey
  Healing isn’t linear. There will be setbacks, pauses, and detours. Compassion is what allows us to keep going when things don’t go as planned. It’s the voice that reminds you progress isn’t measured by perfection, but by showing up again and again, especially when it’s hard. Surround yourself with people who remind you that every step—forward or backward—is part of the process and part of your growth.
• Evocation – Trust Your Inner Wisdom
  You are not broken. The answers you seek often already exist within you. Evocation is the process of drawing that wisdom out, by asking better questions, challenging outdated beliefs, and remaining open to new ways of thinking. A great support system doesn’t try to “fix” you, it helps you uncover what’s already true. From this place of discovery, real and lasting transformation becomes possible.

Together, these pillars form a powerful container for healing, a space where you’re seen, supported, and strengthened as you grow into the healthiest version of yourself. Because while you may be walking your own path, you don’t have to walk it alone.

A Final Word: You Don’t Have to Do This Alone

Healing my gut gave me my life back. But more than that, it gave me myself back.If you’re feeling lost, low-energy, inflamed, or simply off, know this: You are not broken. You are capable of healing.

That’s why I created the 21-Day Gut Reset Challenge, to give you a guided path back to energy, clarity, and vitality, step by step.

If you’re ready, I’d be honored to help guide you to making changes that better support your gut health and your life. 

Click here to learn more and join the 21-Day Gut Reset Challenge

Let’s begin this journey together.

Shawn Chavez
Nationally Board Certified Health Coach

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