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Gastroenterology

Clinical context over quick fix: the fresh consensus on microbiome testing

Microbiome testing
Gastroenterology

A new consensus by 69 global experts redefines the rules of microbiome testing, highlighting strict oversight, comprehensive methods, and crucial patient data to guide clinicians toward reliable gut-health insights.

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Photo HCPs: Clinical context over quick fix: the fresh consensus on microbiome testing

About this article

Author

Dr Amine Zorgani
Created 11 April 2025
Updated 16 April 2025

In recent years, the idea of using gut microbiota as a diagnostic tool has captured the imagination of the medical community. Yet, despite mounting interest, the clinical benefits of microbiome testing remain largely unproven.

A newly released international consensus report 1 has now thrown light on this pressing issue. Spearheaded by 69 experts hailing from 18 countries, the initiative set out to build a clear, evidence‐based framework to guide clinicians and laboratories in adopting standardized microbiome testing practices.

69 experts

18 countries

The right panel

The panel, comprising clinicians, microbiologists, microbial ecologists, computational biologists, and bioinformaticians, embraced the (sidenote: Delphi method A structured process for achieving expert consensus through multiple rounds of anonymous surveys and feedback. ) to forge a set of recommendations. Working in five dedicated groups, the experts tackled general principles, pre-test procedures, microbiome analysis, reporting standards, and clinical relevance. Each statement underwent rigorous scrutiny and was rated on a Likert scale, with an 80% agreement threshold ensuring only robust recommendations made the final cut.

This meticulous process underscored the need for quality assurance measures, multidisciplinary teamwork, and transparent communication regarding the current limitations of microbiome tests. It also highlighted a crucial point: tests should be ordered only on clinical recommendation rather than directly by patients.

The consensus: what you need to know

The below are four recommendations are a MUST for every clinician interested into using the microbiome in their clinical practice. 

  • Ditch Direct-to-Consumer: The consensus strongly discourages patients self-requesting microbiome tests. Testing should ideally be initiated by a physician or licensed healthcare professional with a clear clinical rationale. This highlight concerns over misinterpretation and inappropriate interventions.
  • Beyond F/B Ratio: Forget the (sidenote: Firmicutes/Bacteroidetes ratio A once-popular but now-questioned measure comparing two major bacterial phyla in the gut, often linked (incorrectly) to health or disease. ) ; experts advise against its reporting due to insufficient evidence. Similarly, routine dysbiosis indices lack validation. Focus should be on comprehensive (sidenote: Taxonomic profiling Analyzing a microbial community by identifying and categorizing its members at various taxonomic levels, such as genus or species. ) using 16S rRNA or whole-metagenome sequencing.
  • Clinical Context is King: Reports must include detailed (sidenote: Clinical metadata Essential patient details (e.g., age, diet, medications) that accompany a test sample and help interpret microbiome data in a medical context. ) (age, BMI, diet, medications) to aid interpretation. Comparisons to matched healthy controls are crucial. Surprisingly, testing providers should not offer post-test therapeutic advice; this remains the remit of the referring clinician.
  • Quality and Transparency: High-quality, accredited labs using validated software are essential. Detailed reporting of the entire testing protocol, from sample collection to analysis, ensures transparency.

While acknowledging the promise of microbiome testing for specific conditions, the panel concluded that routine clinical use is not yet supported by sufficient evidence. Further research, including robust diagnostic accuracy studies, is crucial. Clinician training on microbiome science and report interpretation is also vital for future integration. This consensus serves as a crucial roadmap for responsible development and implementation in clinical practice.

Sources

1. International consensus statement on microbiome testing in clinical practice, Porcari, Serena et al., The Lancet Gastroenterology & Hepatology, Volume 10, Issue 2, 154 - 167

Tags
Gut microbiota Clinical microbiome Testing Microbiome standardization Diagnosis Diagnosis guidelines Medical microbiology Microbiome Flora

    See also

    Foundation HUB page An insane discovery: Obelisks new virus-like entities found in human microbes
    Women in Science Day: they make microbiota research! Women in Science Day: they make microbiota research!
    Created 11 April 2025
    Updated 16 April 2025

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