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As promise builds around measuring the gut microbiota to guide disease treatments and personalised nutrition plans, testing must be standardised to enable evidence-based use of diagnostics, say experts.
January 24, 2025
Writing in The Lancet Gastroenterology and Hepatology, a panel of international experts called for a global overhaul of microbiome testing in clinical practice, defining the current state of the market as the “Wild West”, with many tests “totally lacking in meaning and scientific solidarity”.
“The gut microbiota might perhaps one day become a routine tool for the early diagnosis of many diseases and to guide treatment, but at present there is a lack of solid scientific evidence to support these claims,” the group of international professors, medical doctors, and researchers wrote in their consensus paper.
Microbiome testing, they said, urgently needs to be conducted within a global regulatory framework of shared best practices across testing processes, methods of analysis, presentation of results, and potential clinical applications.
The goal? “To pave the way for an evidence-based development of human microbiota diagnostics in medicine,” they wrote.
Speaking to Vitafoods Insights, one of the lead researchers, Gianluca Ianiro MD PhD, from Italy’s Agostino Gemelli University Policlinic and the Catholic University of the Sacred Heart, said the consensus paper was timely for industry – across both medicine and nutrition.
A regulated framework on microbiota testing, Ianiro said, holds promise for both clinical and nutritional settings because the gut microbiota is a key mediator in a number of essential human functions, including metabolism, immune regulation, and drug response.
“To date, we have increasing evidence on the usefulness of personalised medicine and personalised nutrition,” he said. “But we need studies – and we will have [studies] for sure – that show that modifying the gut microbiome by diet in an informed way, by microbiome profiling, rather than without knowing the patient microbiota profile, is useful.”
So, as research in this field advances, it is vital that studies are conducted within a standardised regulatory framework to ensure meaningful data and application in the nutrition and clinical fields, Ianiro said.
Today, Ianiro said there is instead a “plethora of microbiome testing” across countries “without any standardisation”, creating “considerable economic burden and confusion” among patients and clinicians alike.
Writing in the consensus paper, the panel of experts said investigations around using gut microbiota as a tool for diagnosis, prognosis, risk stratification, and response to treatment also lacked scientific evidence. In addition, future doctors are not being taught how to interpret results or manipulate the gut microbiota for therapeutic purposes.
“The market runs faster than the science, as has already happened in the past with home genetic testing,” they said.
Ianiro explained that the hope behind the consensus paper was to overturn all of this and help build out a solid framework to guide scientific findings and clinical indications in gut microbiota research.
“The end goal is to have a standardised framework for microbiome testing, so a clinician can identify a methodologically reliable test,” he said.
The experts presented five key areas to be addressed when developing a standardised framework: the general principles and minimum requirements for providing microbiome testing; procedural steps before testing; microbiome analysis; characteristics of reports; and relevance of microbiome testing in current and future clinical practice.
On the testing and analysis side, Ianiro said standardising methods worldwide “won't be easy” – but it is not impossible, given that most companies working in the field already provide sequencing, which means there should be no hardware issues.
In addition, most companies are also using open-access software for microbiome analysis.
Professor Maurizio Sanguinetti, professor of microbiology at the Catholic University of the Sacred Heart and director of the department of laboratory and haematological sciences at the Agostino Gemelli University Policlinic, said: “This consensus document represents a crucial step towards bringing order to the current panorama of diagnostic tests on the intestinal microbiota.
“The diagnostic characterisation of the intestinal microbiota must be based on rigorous standards, in order to guarantee reliable and clinically useful results. It is not a simple laboratory test, but a complex tool that requires a deep understanding of microbial dynamics and their impact on human health.”
Dr Serena Porcari, first author of the study and part of the unit of gastroenterology at the Agostino Gemelli University Policlinic, agreed.
She said: “In recent years, the intestinal microbiota has taken on a key role as a diagnostic, prognostic and therapeutic tool. From this point of view, the first step, for a targeted modulation of the microbiota itself, is to obtain a standardisation of its analysis, regulated according to the definition of minimum criteria for performing the test.”