Comprehensive Stool Testing
—Metagenomic Stool Testing · Included with the digestive Reset Program
You doctor's stool test showed very little.
This one looks at everything.
Standard stool tests check a handful of markers and call it normal. Shotgun metagenomic sequencing maps your entire gut ecosystem — every bacteria, fungi, pathogen, and metabolic byproduct — giving us the full picture of what’s actually driving your gut symptoms.
Certified Microbiome Analyst | Gold Standard Microbiome Testing | Included in Every Program
100%
of gut genetic material sequenced — not just one or two bacteria
Gold
standard method used in clinical microbiome research worldwide
10+
categories of microbiome data your doctor’s test won’t look at
—What is Shotgun Metagenomic Sequencing?
Most stool tests skim the surface.
This one reads the whole book.
Your doctor’s standard stool test — and even many functional medicine qPCR tests — only look at a narrow selection of predefined targets. They can only find what they’re specifically designed to look for. Which means anything outside that narrow window gets missed entirely. That’s why you keep being told everything looks “normal”.
Shotgun metagenomic sequencing works differently. Instead of looking for specific targets, it sequences every single piece of genetic material in your stool sample — bacteria, fungi, archaea, viruses, parasites, and the metabolic byproducts they produce. It’s the same technology used in clinical microbiome research. And it gives us a true, complete picture of what’s living in your gut and how it’s driving your symptoms.
“As a Certified Microbiome Analyst, I know how to read these results at a clinical depth most practitioners never get to — and how to translate them into a plan that actually fits your life.”
—The visual explanation of metagenomic stool testing
qPCR sees just one slice of the pie.
Metagenomic stool testing sees the whole pie.
qPCR testing
Only tests for a small, predefined set of organisms — like looking at one slice of a pie. If your problem isn’t in that slice, it gets missed entirely. This is why qPCR results come back “normal” while your symptoms tell a completely different story.
Metagenomic Testing
Sequences every piece of genetic material in your sample — the entire pie. Nothing is excluded. Every bacteria, fungi, archaea, virus, pathogen, and metabolic byproduct gets identified and measured. That’s why this test finds what every other test misses.
—The side by side comparison of PCR to Metagenomic stool tests
Not all stool tests are the same.
Here's the breakdown.
Standard PCR / Doctor’s stool test
- Limited panel of predefined targets only
- Misses microbiome diversity entirely
- Doesn’t assess metabolic byproducts
- Can produce false positives
- Can instill “kill the pathogen” mindset — ignoring the importance of overall balance
- Often comes back “normal” while you still suffer from gut symptoms
Shotgun Metagenomic Sequencing
✓Sequences every piece of genetic material
✓Maps full species richness and diversity
✓Identifies all metabolic byproducts — good and bad
✓Assesses the whole ecosystem of your microbiome
✓Gold standard used in clinical microbiome research
—What's Captured in Metagenomic Stool Testing
Several categories of data your doctor's
test never captures.
Keystone beneficial bacteria
Whether your foundational beneficial species are at optimal levels — critical for gut integrity, immune function, and inflammation control.
Pathobionts & opportunistic bacteria
Overgrowths of bacteria that cause significant gut damage and inflammation when they take over — often missed entirely by standard testing.
LPS-producing bacteria
A major driver of gut inflammation, bloating, gas, leaky gut, fatigue, and systemic chronic disease that standard tests never check.
Archaea, yeasts, fungi & parasites
Methanogens, Candida, other fungi, and parasites and infections that conventional testing routinely misses — all of which can drive significant digestive symptoms.
Gas-producing organisms
Methane and hydrogen sulfide producers — the specific organisms behind the bloating, constipation, and diarrhea that nothing else seems to explain.
Harmful gut byproducts
Ammonia, branched chain amino acids (BCAAs), Trimethylamine (TMA), histamine and more — metabolic byproducts that drive inflammation and are invisible to standard testing.
Protective anti-inflammatory byproducts
Butyrate, acetate, and propionate — the short-chain fatty acids your gut needs to maintain the intestinal lining and reduce inflammation.
Species richness & diversity
How your overall microbiome diversity compares to a healthy reference population — one of the most important indicators of long-term gut health.
Beneficial Microbes & Keystone Species
Beneficial bacterial species are critical to gut healing, immune regulation, and inflamation control. We make sure these are present at optimal levels to support healing.
Stool Chemistries & GI Health Markers
Stool pH, secretory IgA, digestive enzyme production, bile acid production, fat digestion, carbohydrate digestion, calprotectin, and occult blood – funcitonal markers that tell us how well your gut is actually working, where diestion is breaking down and whether active inflammaion is present.
—What your metagenomic stool test results can look like
Real data you can apply to your real life.
Creating a clear path forward.
Results that actually tell you something useful.
Most people who’ve had stool testing before have walked away more confused than when they started. Our results review session is different — I walk you through every finding in plain language, connect it directly to your specific symptoms, and explain exactly what we’re going to do about it.
—What Shot Gun Stool Testing Can Address
If your gut is struggling,
the microbiome is almost always part of it.
IBS
Bloating & Gas
Constipation
Diarrhea
Reflux & GERD
Stomach Pain
IBD
Hormone Related Gut Issues
Fatigue & Brain Fog
Autoimmune Conditions
Food Sensitivities
Eczema & Acne
Weight Loss Resistance
Depression & Anxiety
Diverticulosis
Leaky Gut
Why this requires a specialist to interpret
Sarah Neumann Haske, MS, RDN · Certified Microbiome Analyst
Shotgun metagenomic results are complex. Most practitioners who order basic stool tests don’t have the training to interpret this level of data — which is exactly why a Certified Microbiome Analyst certification exists. I’ve spent years learning how to read these results at a clinical depth, understand what the imbalances mean for your specific symptoms, and translate them into a targeted protocol that addresses what we actually find. I’ll translate your results into an individualized, actionable plan.
Ready to Start?
Gut issues your doctor couldn't explain.
Comprehensive stool testing finds what standard testing missed.
Included with every Digestive Reset Program.
Your doctor did standard testing and told you everything looked “normal”. Root cause medicine stops managing your symptoms and actually helps you find relief.
—Not ready to book? Start here — free.
Two free resources to help you understand what’s going on before you spend a dime 👉
—From the Gut Health Blog
Want to understand the microbiome before your call?
Real science on the microbiome. Written for women dealing with real gut issues.
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The Incredible Power of Polyphenols on Your Microbiome
One of the most powerful things you can do for your microbiome is also one of the most overlooked — eating polyphenol-rich foods. Here’s how these plant compounds feed your beneficial bacteria and why they matter so much for gut healing.
Read More About My Exclusive 3 Month Complete Digestive Healing Program Which Includes Shot Gun Stool Testing, & More!
About Sarah
Sarah Neumann Haske, MS, RDN, is a Registered Dietitian Nutritionist with over 20 years of experience, specializing in digestive health for the past decade. She holds a Master’s of Science in Human Nutrition, is a Certified Microbiome Analyst, and is the Owner of Neumann Nutrition & Wellness, LLC. Her practice helps clients heal their gut, using a root-cause approach to their digestive health. As a result of her program her clients are able to come off medications, feel more energized, and be more confident in their bodies again. If you're interested in being a partner in your own health journey and finding the direction and accountability you need to reach your digestive health goals, then schedule your digestive assessment call with Sarah here.