How to successfully commercialise microbiome-based diagnostics

Andrew Thomson, Brian Carpenter and Robert Broadnax from the global consulting firm Charles River Associates (CRA) explore key drivers of adoption of microbiome-based diagnostics, highlight barriers to their use and offer recommendations to overcome specific challenges.

Microbiome-based diagnostics have generated significant interest in recent years partly due to widespread advances in the development of underlying microbiome mapping technologies. These technologies can link the composition of a person’s microbiome – the diverse community of all microorganisms, helpful and harmful, in the human body – to the emergence and progression of specific diseases (e.g., irritable bowel syndrome [IBS], inflammatory bowel disease [IBD], and Celiac disease). Arming physicians and patients with tools to accurately characterise imbalances in bacteria living in the human microbiome (dysbiosis) is essential to identifying and managing diseases as early as possible. 

There is still an unmet need for therapeutics that can restore a harmonious microbial ecosystem (symbiosis) to treat a range of diseases, but several promising therapies are approaching potential FDA approval. Developers of microbiome-based diagnostics must prepare for the emergence of these therapeutics as they will likely accelerate the need for complementary diagnostics. They must understand the impact impending therapeutics will have on the microbiome market and characterise the depth and breadth of the commercial opportunity, especially as advanced underlying technologies allow diagnostics to serve a range of uses across therapeutic areas.

Drivers of adoption

The potential uses of microbiome-based diagnostics range from precise clinical diagnosis of diseases to day-to-day wellness tracking with direct-to-consumer (DTC) tools. The following drivers will be essential in supporting adoption of microbiome-based diagnostics for these and other uses.

• Early disease detection and diagnosis: As researchers better understand the relationship between the microbiome and specific diseases, diagnostics will be able to detect and/or diagnose diseases, allowing for early prevention and treatment strategies.
• Non-invasive option: Many diagnostics on the market or in development offer convenient, non-invasive and at-home sampling for patients. They are positioned to potentially replace more invasive diagnostic options for specific diseases, such as replacing endoscopies and colonoscopies in IBS and IBD.
• Personalised therapeutics recommendations: Many microbiome-based diagnostics provide personalised and precise information on a patient’s microbiota health and function and can even provide action-items for tailored treatment interventions (e.g., use of probiotic therapies, dietary interventions or lifestyle changes). These diagnostics may play a role in improving precision medicine, especially as microbiome-based therapies become available.
• Applications along the patient journey: Increased funding and interest in the research and commercialisation of microbiome diagnostic tools has led to development of advanced and relatively low-cost technologies that can be used by consumers and in the clinic (physician-ordered). There is a growing number of patients ordering low-cost DTC tests that are easily administered at home to monitor their health conditions. These tests can be ordered online, shipped to a patient’s home, and administered in a straightforward way, providing interpretable reports with personalised diet and lifestyle recommendations that can identify early signs of disease. Concurrently, more physicians are ordering higher-powered microbiome tests for their patients to support diagnosis of chronic unresolved gut symptoms, especially late in the patient journey, following failure of traditional diagnostic tools.

Barriers to use

While the interest and need for microbiome-based diagnostics is growing there are some concerns that could hinder their adoption. 

• Lack of evidence: There is a lack of consensus and clarity about how imbalances in the microbiome ultimately impact human health and cause disease, prompting questions about the reliability of diagnostic tools. There are also no clear standards for microbiome-based diagnostics research, technology development and product functionality. Test results delivered to patients at home may be skewed by irregularities in sample preparation and testing, which can lead to dramatic differences in diagnostic results. As a consequence, many companies remain cautious and compromise on claims about their product’s capabilities, choosing to focus on health and wellness claims until they generate evidence to support clinical diagnostic claims verified by the FDA.
• Undefined intervention points: Physicians and patients are also not aligned on where and how diagnostic tools should be used along the patient journey (e.g., as a routine test, upon presentation of specific disease symptoms, before and after a dietary change). This lack of consensus is exacerbated by the fact that there are different tools available and end-users often have a limited understanding of these products, their underlying technologies and differentiating factors.
• No approved therapeutics: Without any FDA-approved microbiome-based therapies, the value of microbiome-based diagnostics is diminished. Currently, there are only a few actionable treatment interventions that can be effectively informed by personalised diagnostic tools. Microbiome-based diagnostics will likely continue to be used on a DTC basis until physicians have microbiome-based therapies available.
• Unclear regulatory pathways: There is no clear path towards regulatory approval for microbiome-based diagnostics (or therapeutics), causing developers to pursue multiple different routes such as FDA 510k clearance and a laboratory-based pathway.
• Limited insurance coverage: Reimbursement for most microbiome-based diagnostics is absent. Tests are rarely covered by state or private insurance schemes as payers are not yet convinced of their clinical value or cost-effectiveness. As a result, many patients must pay out-of-pocket, pushing them to opt for less expensive DTC tools rather than often higher-cost tests ordered by physicians. 

Recommendations for developers

The barriers above highlight the need to communicate the clinical and economic value of microbiome-based diagnostics and elevate their use above DTC health and wellness applications and into the clinic. Diagnostics developers will need to convince stakeholders, ranging from patients to payers, of the value diagnostic tools present in improving patients’ wellbeing and outcomes, through more appropriately targeted microbiome-based therapeutics. A critical element of this perception shift will be linking test results from diagnostics with microbiome-based treatment interventions (once available), providing the opportunity for microbiome-based diagnostics to inform targeted use of therapeutics and strengthen their clinical value. 

This will require diagnostics developers to systematically: 

1. identify and understand opportunities that present the highest commercial potential for diagnostic technologies; 
2. develop convincing value propositions that align with unmet needs, can be sufficiently supported by data, and resonate with stakeholders; 
3. implement a range of market-shaping techniques to build awareness and demand for these diagnostics;
4. establish compelling positioning versus the competition; 
5. develop and execute a robust evidence generation strategy outlining how to identify and prioritise data gaps relevant to a diagnostic’s value proposition (e.g., patient outcomes data and health economics data); and 
6. effectively communicate a product’s value proposition to target customers once all required data are collected through marketing and field efforts.

The views expressed herein are the authors’ and not those of Charles River Associates (CRA) or any of the organisations with which the authors are affiliated.