Significant variability in the microbiome research methods that inform treatments for gastrointestinal diseases has been exposed by a major international study led by the UK’s Medicines and Healthcare products Regulatory Agency (MHRA).
The findings have highlighted an ‘urgent need’ to establish unified standards for global gut microbiome research, the MHRA has said.
Published in the journal mSystems, the study involved 23 laboratories from 11 countries across four continents testing identical samples of gut microbiome bacteria. Results varied dramatically between labs, with species identification ranging from 63% to 100% accuracy. This means that some labs failed to detect a third of the bacterial species present in the sample.
False positive rates ranged from 0% to 41%, meaning that some labs incorrectly identified bacteria that weren’t present in the sample. And diversity estimates also varied with some labs identifying as few as 12 bacterial species while others found as many as 185.
Ensuring accuracy of detection methods
These results have ‘undermined confidence’ in the field of microbiome research, which increasingly informs treatments for gastrointestinal conditions such as inflammatory bowel disease, metabolic syndrome, irritable bowel syndrome and colorectal cancer.
However, the study also establishes Minimum Quality Criteria for four key reporting measures that labs can now use to validate their microbiome analysis methods.
This means that labs worldwide can assess the accuracy of their own detection methods so that future gut health research will be more reliable.
As a result, medical treatments based on microbiome science will be more trustworthy and progress towards new therapies for gut-related diseases should accelerate.
Indeed, the researchers highlighted that this first-of-its-kind global study not only comprehensively tested methodologies used by leading laboratories across the world to reveal the reality of the bias in the field, but also provided avenues for workflow optimisation to accelerate innovation and translational research to move the field forward.
Supporting diagnosis and treatment with microbiome research
The MHRA told the public that the study has helped ‘to ensure that when doctors or researchers analyse your gut health, they’re getting accurate information – which means better diagnosis and treatment for everyone’.
Lead author of the study and senior research and development scientist at the MHRA, Saba Anwar, commented: ‘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.’
The research was commissioned and funded by the Department of Health and Social Care Policy Research Programme through the MHRA Regulatory Science Research Unit, with additional support from an Innovate UK Small Business Research Initiative Award for ‘Creating Standards for Microbiome Therapies’.