Why I Broke Up with the GI-MAP Test

For the past nine years, the GI-MAP stool test was a staple in my practice. Like many functional medicine practitioners in the U.S., I used it to help patients understand what was happening in their gut. It felt like the best tool we had.

But this year, after completing a 90-hour intensive training in microbiome medicine with Jason Hawrelak, ND, I realized it was time to break up with GI-MAP.

Here’s why.

PCR vs. Shotgun Sequencing: What’s the Difference?

The GI-MAP uses quantitative polymerase chain reaction (qPCR). You may recognize this technology because it’s also used in COVID nasal swab tests.

qPCR was a step up from the stool tests your conventional doctor orders, which rely on culture techniques — old-fashioned growing bacteria in a dish.

qPCR is more sophisticated. It detects the unique genetic signature (DNA or RNA) of specific pathogens. But there’s the catch: it only finds what it’s designed to look for. It does not map the entire ecosystem.

Shotgun sequencing does.

Shotgun metagenomics is the gold standard in microbiome analysis. This method sequences all the genetic material (DNA) present in stool, capturing the full microbial landscape: bacteria, archaea, viruses, fungi, parasites — over 120,000 different microbes in total.

It doesn’t just identify pathogens. It reveals the whole ecosystem:

• The beneficial microbes that regulate hormones, metabolism, mood, and immunity
  
• Keystone species humans evolved with that may now be extinct in modern guts
  
• And the highly inflammatory, disruptive microbes that should not be there at all
  

Why It Matters

Most practitioners aren’t trained to interpret shotgun sequencing. Without advanced training, the data is overwhelming. With my recent certification, I can now analyze how the ecosystem is functioning as a whole — and that’s where the clinical breakthroughs happen.

In practice, this means I can see:

• Which beneficial microbes are thriving, missing, or extinct
  
• How balanced the ecosystem is across bacteria, fungi, and viruses
  
• Where inflammatory microbes are driving symptoms that show up as “hormonal,” “digestive,” or “autoimmune”
  

What I’m Seeing

So far, I’ve run dozens of shotgun sequencing tests for patients. The patterns are sobering:

• Nearly everyone is scoring between 50 and 85 out of 100 on microbial health.
  
• Truthfully, we should all be in the 90th percentile or higher. That’s the target I set with my patients.
  
• Many people are low in beneficial microbes — some have completely lost ancestral keystone strains.
  
• And in too many cases, I’m identifying disruptive, inflammatory microbes that simply don’t belong in a healthy ecosystem.
  

None of this is surprising, given the impact of antibiotics, our obsession with sterility, nutrient-poor diets, and reduced exposure to nature. But it is alarming.

This is why restoring the human microbiome isn’t optional — it’s essential for our health and for the generations that follow.

Practical Advantages

Beyond the depth of insight, the test I now use is also more practical for patients:

• Cost: $199 (less than the GI-MAP)
  
• Collection: simple swab (no messy vials)
  
• Results: slower turnaround, but far more valuable

The Bottom Line

The GI-MAP had its place, but it no longer gives me the level of information I need to truly support patients. With shotgun sequencing, I can finally see the bigger picture and help my patients move toward the microbial resilience we should all have.