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Five Challenges Limiting Widespread Adoption of Microbiome-Based Diagnostics

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As several microbiome-based therapeutics, which manipulate and restore the body’s gut bacteria, advance toward potential FDA approval, developers of microbiome-based diagnostics are preparing for their launch. These diagnostic technologies can link the composition of a person’s microbiome to specific diseases (e.g., inflammatory bowel disease (IBD), Celiac disease, etc.), allowing for early disease prevention and treatment. Despite increasing global efforts to develop and commercialize microbiome-based diagnostics in recent years, a new analysis outlines five challenges hindering their broad adoption. To overcome these challenges, developers of microbiome-based diagnostics will need to understand the impact that emerging therapeutics will have on the market, pending approval, and characterize the depth and breadth of the commercial opportunity, especially as underlying microbiome mapping technologies quickly advance and diagnostics can be used across a range of therapeutic areas.

Figure 1: Microbiome-based diagnostics patient journey. Source: CRA market research and analysis. 

Assessing the current microbiome diagnostic landscape

The potential uses of microbiome-based diagnostics range from precise clinical diagnosis of disease to day-to-day wellness tracking with direct-to-consumer (DTC) tools. These diagnostics will also allow for targeted use of microbiome-based therapeutics by healthcare providers seeking to restore symbiosis (or a harmonious microbial ecosystem) in their patients.

At the DTC level, developers are targeting health-conscious consumers who are increasingly showing interest in the potential role of the microbiome in improving overall health. Several developers of DTC tools provide microbiome tests that can help predict health parameters including digestion, metabolism, sleep and focus, based on an individual’s gut bacteria profile. Some also use proprietary machine-learning algorithms to develop personalized reports for customers, which can assess data from multiple sources such as genetic profile, diet and blood biochemistry.

Table 1:
Select DTC microbiome diagnostic tools

Source: CRA market research and analysis. Note: This table is not exhaustive; additional developers with similar DTC products, but less market presence, include Biomes (Germany), Atlas Biomed (UK), Elsavie (Estonia).

1 Microba collaborates with SYNLAB laboratory services to provide MyBiome in Europe.

2 Viome also partners with Mayo Clinic and GSK to develop precision nutrition machine learning algorithms.

Beyond DTC use, developers of microbiome-based diagnostics also seek to arm physicians (rather than patients) with tools to improve diagnosis of specific diseases in a variety of applications. These applications include non-invasive diagnosis of IBD and irritable bowel syndrome (IBS), identification of precancerous and cancerous lesions, and monitoring of disease progression for diseases such as colorectal cancer, which is typically tracked through invasive procedures like colonoscopies.

Table 2
: Selected physician-ordered microbiome diagnostic tools

Source: CRA market research and analysis. Note: This table is not exhaustive; CRA has highlighted tests with the largest available body of supporting evidence.

1 Genetic Analysis has partnered with Bio-Rad, Luminex, BIOHIT Healthcare, and Synlab to develop GA-Map.

2 Enterome has partnered with Nestlé Health and AbbVie to develop biomarker tests.

3 Metabiomics has partnered with Prescient Medicine, Janssen, Mayo Clinic, George Mason University, and Kaiser to develop the LifeKit test.

*NAFLD: Nonalcoholic fatty liver disease; NASH: Nonalcoholic steatohepatitis

Five barriers to adoption of microbiome-based diagnostics

With several factors supporting adoption of microbiome-based diagnostics – including the opportunity for early disease detection and diagnosis and their positioning as a convenient, non-invasive option for patients – there are five primary concerns that could hinder their broad adoption among consumers:

1.       Lack of clear evidence or product standards

There is a general lack of consensus and clarity among industry stakeholders about how microbiome manipulation may ultimately impact human health and treat different diseases. The microbiome sector is still in its nascent stages and many stakeholders are calling for additional clinical data supporting this therapeutic approach. These concerns are prompting questions about the reliability of microbiome-based diagnostic tools. There are also no clear standards for microbiome-based diagnostics research, technology development and product functionality, which presents challenges. Many companies remain cautious in terms of their marketing and business strategies and compromise on claims about a product’s capabilities, choosing to focus on health and wellness claims until they collect data to support clinical diagnostic claims verified by the FDA.

2.       Undefined diagnostic intervention points

There is no widely accepted consensus among physicians and patients on where and how diagnostic tools should be used along the patient journey, for example, as routine tests, upon presentation of specific disease symptoms, or before and after a dietary change. Many end-users also do not understand how these diagnostic tools work, their underlying technologies and differentiating factors, making them hesitant to adopt.

3.       Lack of available therapeutics targeting the microbiome

A primary argument against use of microbiome-based diagnostics is the lack of FDA-approved microbiome-based therapies. Currently, there are only a few actionable treatment interventions that can be effectively informed by personalized diagnostic tools. Current interventions often revolve around general wellness approaches, for example, dietary and lifestyle changes and over-the-counter probiotics. As a result, microbiome-based diagnostics will likely continue to be used on a DTC basis until physicians have microbiome-based therapies available to complement them.

4.       Unclear regulatory pathways

Another factor limiting the adoption of microbiome-based diagnostics is the lack of clear regulatory pathways for these products. As a result, developers are pursuing multiple different routes including FDA 510k clearance and a laboratory-based pathway. It is essential that diagnostics developers collaborate with the FDA and other regulatory bodies as early as possible in the development process to align on the regulatory requirements for approval, including the level of supporting clinical data needed.

5.       Limited insurance coverage

The lack of reimbursement for most microbiome-based diagnostics presents another challenge. Microbiome-based diagnostic tools and tests are rarely covered by state or private insurance providers as payers remain uncertain of their clinical value or cost-effectiveness (largely due to the barriers described above). This forces many patients to pay out-of-pocket, and thus incentivizes them to choose less expensive DTC tools rather than often higher cost, but potentially more effective tests ordered by physicians in the clinical setting.

These barriers highlight the need to effectively demonstrate and communicate the clinical and economic value of microbiome-based diagnostics and generate data supporting their use over DTC health and wellness applications. Adoption will largely depend on the ability of developers to convince industry stakeholders, ranging from patients to payers, of the value of microbiome-based diagnostics and their potential to improve patient outcomes and quality of life. They will also need to show the opportunity for microbiome-based diagnostics to inform targeted use of microbiome-based therapeutics (once available) and improve precision medicine.

Recommendations for successful commercialization

In order to drive adoption, developers of microbiome-based diagnostics will need to enter the market systematically, following the six steps below:

1.       Identify the commercial opportunity: Diagnostic developers must establish an in-depth understanding of the commercial potential of their products, considering factors including the strength of a product’s clinical value, the size of the target patient population, likelihood of physician and patient adoption and payer reimbursement, the level of competition, and opportunities to complement pending microbiome-based therapeutics.

2.       Demonstrate a product’s value proposition: Developers must clarify a product’s value proposition and ensure it aligns with the needs of target customers, is supported by real-world data, and resonates with key stakeholders.  

3.       Develop the market: Generating demand for microbiome-based diagnostics will be critical in ensuring successful market entry and likely require input from a range of stakeholders. This might involve educating customers, including physicians and patients, about the microbiome in general, its impact on human health, and how a microbiome-based diagnostic works.

4.       Showing differentiation versus competitors: The microbiome sector is rapidly growing, meaning there is more competition. It is essential that diagnostic developers differentiate their product from existing competitors and future products to support consumer uptake post-launch.

5.       Effectively generate required data: As described above, adoption of microbiome-based diagnostics is currently hindered by a lack of supporting data and of available microbiome-based therapeutics tied to these diagnostics. Developers must create a robust evidence generation strategy detailing how they will identify and address data gaps regarding a diagnostic’s value proposition. This might involve conducting retrospective claims analyses, prospective chart studies, health economic and patient outcomes studies, and additional clinical trials.

6.       Communicate the value proposition: Once all required data are collected, developers must effectively communicate a diagnostic’s value proposition with target customers, tailoring any efforts to the needs of a product.

There is more research to be done to further establish the connection between the microbiome and human health. As technological advances continue and microbiome-based therapeutics get closer to regulatory approval, the value of complementary microbiome-based diagnostics will crystallize as the need for these products grows in the years ahead.

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

Andrew Thomson is a consulting associate in the Life Sciences Practice at CRA with 4+ years of experience in commercial strategy consulting with pharmaceutical and biotech clients alike, focused on microbiome-based healthcare solutions.

Brian Carpenter is a principal in the Life Sciences Practice at CRA with 10+ years of biotech experience and extensive experience in commercialization strategy for microbiome-based therapeutics and diagnostics.

Robert Broadnax is a vice president in the Life Sciences Practice at CRA with 20+ years of commercialization experience, focused on commercial strategy for microbiome-based therapeutics and diagnostics.