NEW YORK – An international group of scientists published a set of best practices related to microbiome testing for clinical implementation in response to what they described as a lack of solid scientific evidence underlying current commercially available tests.
The consensus statement, led by researchers at Italy's Fondazione Policlinico Gemelli and the Università Cattolica del Sacro Cuore and published Thursday in the Lancet Gastroenterology & Hepatology, lays out a regulatory framework with recommendations for the indications, analytic methods, presentation of results, and potential clinical applications of diagnostic and prognostic microbiome testing.
The authors pointed to several knowledge gaps that currently impede the clinical use of microbiome-based tests. These include the complexity of the microbiome and its associated sequencing datasets, difficulties in disentangling correlation from causation, the reliance on preclinical models with low generalizability to humans, the limited knowledge most clinicians have about this field, the absence of any validated microbiome test enabling therapeutic follow-up, and the lack of established regulations and frameworks for clinically translating microbiome research.
Despite these barriers, the investigators note that microbiome testing has gained popular interest among many patients, in tandem with a growing field of direct-to-consumer (DTC) microbiome testing companies.
The growth of such companies in the absence of any standardized testing framework, the authors write, raises concerns related to factors such as wasted patient and healthcare system resources, offering patients false hope, and the inability of many physicians to interpret and act upon microbiome test results.
The investigators laid out 35 statements related to ethical, organizational, and technical rules for the development, commercial use, and clinical implementation of microbiome tests.
General recommendations include that microbiome test providers should communicate a "reasonable, reliable, transparent, and scientific representation" of a given test, ensuring that consumers are fully aware of the scarce evidence for its applicability in clinical practice; that any change in an individual's clinical management due to microbiome testing be made only by their referring physicians or healthcare professionals; and that test providers maintain validated and up-to-date computational software pipelines and microbial databases.
"To avoid patients going outside the boundaries of evidence-based clinical medicine, we discouraged the suggestion of treatments within the report," the authors wrote, adding that they see this as a common feature of available tests.
Procedural recommendations include that direct requests for microbiome testing by patients without a clinical recommendation should be discouraged; that patients should not suspend their therapy or change their usual diet before testing, unless recommended by their referring physician; and that key clinical patient data that might influence gut microbiome characteristics should be collected. Such data should at least include age, gender, body mass index, dietary habits, smoking and alcohol status, gut transit time, comorbidities and medications, and past medical history.
The investigators also recommend that a patient's microbiome composition be described with the "deepest possible taxonomic resolution" and be measured longitudinally, while cautioning that we currently lack enough information to accurately state healthy reference ranges for the relative abundance of most microbial species.
With respect to the relevance of microbiome testing to clinical practice, the researchers state that not enough evidence currently supports the routine use of such testing and that although qualitative and quantitative data found in microbiome reports could manage several disorders, there is not yet enough evidence to apply these in clinical practice.
The report also highlights the paucity of legal frameworks surrounding the use and protection of patient data generated by microbiome testing. The lack of defined regulatory standards or authorities for microbiome testing raises issues related to the legal framework regarding personal data use within the country where testing is occurring, the potential for data to be used beyond the remit of what is reported to the patient (such as by selling data to commercial entities), and the possibility that different aspects of an overall microbiome test might be done in different laboratories, each with their own policies related to personal data management.
The investigators noted in their statement that one key long-term objective of their report is to guide future research on how to develop and apply clinical microbiome-based tests, as this is a field with considerable potential. They noted that any studies that strengthen our understanding of the diagnostic potential of the microbiome must also be paired with educational efforts for clinicians.
"We recognize," the authors wrote, "that due to the advancement of technologies and the increase in pertinent evidence, our recommendations might become outdated quickly, but we are also confident that our guidance framework will remain reliable over time."