Is Shotgun Sequencing Better Than PCR?

The Lab Report

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Stool testing technology has advanced rapidly in recent years, with newer methods like PCR and whole-genome sequencing offering faster and more precise insights into the gut microbiome. These innovations have transformed how clinicians approach gut health, allowing for more targeted interventions. However, older technologies—such as microscopy, culture, and enzyme-based assays—still play a valuable role. These methods provide functional insights that molecular tools may miss, such as direct observation of parasites or assessment of digestive markers. The most comprehensive labs recognize that no single method gives the full picture. Instead, combining the strengths of both modern and traditional techniques ensures more accurate, clinically meaningful results.

In this episode, we dive into the pros and cons of different laboratory methodologies used in stool testing—from culture and microscopy to PCR and advanced sequencing. We break down how these choices impact accuracy, sensitivity, and clinical usefulness. You'll also learn why Genova Diagnostics stands out for its integrative, evidence-based approach, combining multiple testing methods to deliver the most comprehensive and clinically actionable results available.

Today on The Lab Report:

4:00 Technology grows quickly, and the microbiome is complex
7:30 Microbiology culture
12:40 PCR – very precise if done correctly!
17:00 Interpreting the laundry list
20:10 Remember the microscope?
23:30 Whole-genome (shotgun) sequencing pros/cons
27:15 Genova does it all – and well

Additional Resources:

GI Effects Stool Profile

Microbiomix

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