Do Good Poops = A Healthy Gut? Not Always.

I’m a little late to the party (but still celebrating anyway): World Microbiome Day (June 27). 

World Microbiome Day is the perfect time to bust one of the biggest myths in gut health:

🚫 If you poop every day and it looks good, your gut microbiome must be healthy.

Sure, regular, well-formed bowel movements can be a good sign. I absolutely want clients paying attention to what’s in the toilet bowl! But here’s the twist: your gut can look fine on the outside and still be struggling under the surface.

Newer stool testing methods, and especially shotgun sequencing (like what we use in The Gut Lab), are revealing a far more complex picture.

Even if you’re going daily, no bloating, and your poop is a perfect 4 on the Bristol scale… you could still have gut-related imbalances driving things like:

• Eczema, acne, or allergies
• Headaches or migraines
• Fatigue or brain fog
• Anxiety or mood swings
• Hormonal issues or poor detox
• Autoimmune flares

These issues aren’t always digestive. But the gut’s influence extends way beyond digestion.

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So What Is Shotgun Sequencing?

Most stool tests look for a short list of microbes—around 60 or so. But shotgun sequencing scans for over 120,000 different microbes and gives insight into what they’re actually doing, not just who’s there.

With this kind of test, we can see:

• Hidden pathogens (like one client whose test revealed botulism or another that revealed Vibrio, that other labs had missed)
• Signs of gut inflammation or healing
• Fungal and viral overgrowth
• Leaky gut risk
• How well your gut might bounce back after antibiotics
• Whether your microbes are producing helpful or harmful compounds (like anti-inflammatory molecules like butyrate and GABA, or inflammation-driving histamines and lipopolysaccharides)
• Estrogen recycling and detox risks
• Even antibiotic resistance genes

It’s a deep dive into the full ecosystem of your gut—not just a snapshot.

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TLDR: Your poop might look perfect, but that doesn’t mean everything is running smoothly inside.

Think of it like a shiny red apple that looks great… until you take a bite and find it’s rotten inside. That’s what can happen when we rely on poop appearance alone to gauge gut health.

If you’re dealing with symptoms that no one seems to connect—or that aren’t getting better—your gut might be the missing link.

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Ready to Look Deeper?

Join me in The Gut Lab, where we use advanced tools like shotgun sequencing to uncover what’s really going on in your gut—and how it’s connected to everything from your skin to your mood to your nutrition to your hormones.

We’ll rebalance your gut, support your nutrition, and calm your nervous system so your body can finally heal.

👉 Click here to book a free “What’s Up With My Gut?” call and see if The Gut Lab is the right fit for you.