The second episode of the Precision Protocol Series from Biocanic, hosted by Jeremy Malecha with co-host Brendan Vermeire of Metabolic Solutions, tackled a topic that has exploded in popularity: stool testing. With new technologies, direct-to-consumer kits, and bold marketing claims, many practitioners are left wondering which tests truly deliver clinically meaningful data and how to interpret results effectively for client care.

This conversation cut through the noise to provide clarity on what stool testing can reveal, where it falls short, and how to use it responsibly in practice.

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The Evolution of Stool Testing

Brendan began by reflecting on how far stool testing has come in the last decade. Earlier methods relied on microscopy, where technicians visually examined stool samples for parasites or fungal overgrowth. While groundbreaking at the time, these tests lacked sensitivity and often missed critical information.

The introduction of PCR (polymerase chain reaction) technology marked a turning point. PCR made it possible to detect microbial DNA and determine the presence or absence of specific pathogens with far greater accuracy. Quantitative PCR (qPCR) advanced this even further, providing measurable data rather than simple positive or negative results.

More recently, shotgun metagenomics and whole genome sequencing have emerged, offering the ability to map entire microbial ecosystems at unprecedented resolution. Yet, as Brendan noted, “technology has surpassed our understanding,” meaning the sheer volume of data often outpaces the research needed to interpret it clinically.

Making Sense of the Data

For practitioners, the challenge is not just accessing stool testing but translating results into actionable care plans. Brendan emphasized that while these technologies can identify hundreds of microbial species, not every data point carries equal weight.

“There is no universally agreed upon definition of what a healthy microbiome looks like,” he explained. While greater diversity generally correlates with better health outcomes, many findings remain ambiguous. The presence of certain microbes, once labeled harmful, is now being reconsidered. For example, organisms like H. pylori or Blastocystis hominis, historically viewed as pathogens, may play neutral or even beneficial roles depending on the host and context.

Because of this complexity, Brendan cautioned against a “microbial whack-a-mole” approach where practitioners focus on eradicating every organism flagged on a test. Instead, he recommended zooming out to look at the bigger picture: overall diversity, key inflammatory markers, and clinical symptoms rather than isolated microbes.

Three Key Categories of Stool Testing

During the episode, Brendan outlined three main categories of stool testing technologies:

1. Microbiome Sequencing
   This includes 16S rRNA sequencing, qPCR panels like GI-MAP, and shotgun metagenomics platforms such as BiomeFX. These tests identify microbial species and, in some cases, estimate functional potential like short-chain fatty acid production.

2. Intestinal Biomarkers
   Markers such as calprotectin, lactoferrin, and zonulin assess gut inflammation, permeability, and immune activation. Among these, calprotectin remains the most validated and widely used in both conventional and functional medicine.

3. Metabolomic Analysis
   Some tests measure metabolites like short-chain fatty acids or bile acids directly, often using mass spectrometry. These provide insights into microbial activity rather than just composition.

Brendan noted that while sequencing data is interesting, “inflammation markers often carry more clinical weight.” For example, a client whose calprotectin levels drop from 200 to 20 after an intervention shows clear improvement, regardless of whether specific microbes fluctuate on a sequencing report.

Practical Application in the Clinic

So how should practitioners integrate stool testing into client care? Brendan shared a layered approach:

• Start with intestinal health markers. Determine whether there is inflammation, impaired digestion, or intestinal permeability before focusing on microbiome composition.

• Use sequencing data for context, not absolute answers. Diversity metrics, phyla ratios, and keystone species like Faecalibacterium prausnitzii or Akkermansia muciniphila provide clues about ecosystem health, but results must be interpreted alongside symptoms and other labs.

• Track changes over time. Retesting after targeted interventions helps reveal whether clinical improvements align with biomarker shifts.

One case study discussed in the episode illustrated this approach well. A client with elevated calprotectin and low diversity underwent targeted gut-healing interventions. On retesting, her calprotectin levels dropped significantly, and microbial diversity increased by 51 species. This alignment between clinical outcomes and lab markers provided confidence that the protocol was working.

Avoiding Common Pitfalls

The conversation also highlighted common mistakes practitioners make with stool testing:

• Overinterpreting single results: Microbial populations can fluctuate daily. One snapshot should not drive long-term protocols.

• Chasing pathogens without context: The presence of an organism does not always mean it is harmful or needs eradication.

• Relying on one test type alone: Combining inflammatory markers with sequencing data offers a fuller picture than either provides alone.

Brendan stressed the importance of client communication as well. Lab results should empower rather than alarm. “We want to avoid fear-based interpretations,” he noted, especially when science around certain markers remains unsettled.

The Future of Stool Testing

Looking ahead, both hosts expressed excitement about emerging technologies that may soon allow real-time gut health monitoring. From smart toilets analyzing inflammatory markers to advanced multi-omics platforms integrating genetics, metabolomics, and microbiome data, the field is evolving rapidly.

For now, the goal is to use current tools wisely—pairing validated biomarkers with clinical context to guide personalized, effective interventions.

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Key Takeaways

• Stool Testing Has Evolved Rapidly

• Diversity Matters More Than Individual Microbes

• Three Main Categories of Testing –

  • Microbiome Sequencing (16S, qPCR, shotgun metagenomics)

  • Intestinal Biomarkers (calprotectin, lactoferrin, zonulin)

  • Metabolomic Analysis (short-chain fatty acids, bile acids)

• Clinical Application Requires a Layered Approach

• Common Pitfalls to Avoid – Overinterpreting single results, treating every detected microbe as harmful, and relying on one test type alone.

• The Future is Real-Time Gut Health Monitoring

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This was only a fraction of the insight shared in the Precision Protocol Series episode with Brendan Vermeire. In the full conversation, we dive deeper into stool testing, which tests are worth your time with clients, the truth behind the results and have to use these tests effectively within your practice.

📅 RSVP for upcoming episodes and catch the replays on YouTube.

Watch the Full Interview