An international study led by the Medicines and Healthcare products Regulatory Agency (MHRA) has revealed significant variability in how laboratories worldwide analyse gut microbiome samples, underscoring a pressing need for standardised quality measures in microbiome science.
Key findings
23 laboratories from 11 countries across 4 continents were asked to use the newly developed World Health Organization (WHO) International Reference Reagents – containing DNA of known bacterial compositions – to determine whether the methodologies were suitable. When they analysed these samples:
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Species identification varied from 63% to 100% accuracy across different methods, meaning that some laboratories failed to detect a third of the bacterial species present in the sample
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False positive rates ranged from 0% to 41%, meaning some labs incorrectly identified bacteria that weren’t present in the sample
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Sample diversity estimates varied considerably, with labs identifying as few as 12 or as many as 185 different bacterial species in the same sample
Why this matters
The gut microbiome is increasingly implicated in conditions treated or of interest to aesthetic-medicine practitioners - such as metabolic syndrome, inflammation, skin health and overall wellness. The study’s findings suggest that without uniform standards, results from microbiome analyses may be inconsistent, undermining confidence in both diagnostics and treatment decisions based on such data.
What the study identified as sources of variation
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Choice of DNA‐sequencing technology
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Bioinformatics software and reference databases used
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Versions of reference databases (even minor updates had significant impact)
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Lab protocols and techniques
Interestingly, the research showed that one laboratory achieved high‐quality results using around 890,000 DNA sequence reads, while others used an average of 25.4 million reads, suggesting efficient methods are possible.
Moving the field forward
As a result of this work, the MHRA and international collaborators have established Minimum Quality Criteria for four key reporting measures in microbiome analysis. The WHO International DNA Gut Reference Reagents are now available globally for laboratories to benchmark performance and optimise methodology.
Implications for aesthetic medicine practitioners and clinics
For practitioners involved in aesthetic, wellness or metabolic-health medicine, this study highlights that:
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Microbiome analyses used to guide treatments (e.g., for metabolic optimisation, gut health, skin‐gut axis considerations) may vary significantly in accuracy depending on the lab and methodology used.
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Before relying on microbiome test results to guide interventions (supplements, diets, lifestyle prescribing, adjunct therapies), it is worth checking whether the laboratory follows reference standards or validated methods.
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As the field advances, using validated microbiome tests tied to robust quality criteria will be important to maintain clinical confidence and patient safety.
By exposing the scale of methodological variation in global microbiome research, the MHRA-led study confirms the urgent need for harmonised standards. As the study authors note:
“This benchmark study highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents to elevate the quality of data in microbiome research. By pinpointing the sources of bias in existing methodologies using reference reagents, we can accelerate innovation and method optimisation.”
For the aesthetic-medicine sector, where gut-health, metabolism and wellness are increasingly part of the treatment ecosystem, this research offers a timely call to ensure that any microbiome-based tools or diagnostics used are underpinned by rigorous, validated methodologies.
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