Unleashing the Power of the Microbiome: Advancements, Challenges, and the Therapeutic Future

The human microbiome has been shown to play extensive roles in health and disease. Many new therapeutics are being developed to leverage the microbiome to treat a wide range of diseases. This innovation is burdened by the host of manufacturing, regulatory, and other challenges facing drug developers. Contract development and manufacturing organizations (CDMOs) with experience in the production of microbes as therapeutics will play a key role in enabling realization of the full potential of this emerging field. List Labs, with decades of experience and the ability to provide end-to-end support at clinical and commercial scale, is positioned to be a leading outsourcing partner for developers of microbiome-based live biotherapeutic products (LBPs) and other live bacterial therapeutics.

Role of the Microbiome

The human microbiome is established at birth and develops in response to diet, drug use (most notably antibiotics), and environmental conditions, and according to the genetic makeup of the individual. There could be as many as 100 trillion microbes living in each person, and their genes (microbiome) make up what is considered to be a second genome.1

These commensal, symbiotic, and pathogenic microorganisms are largely present in the nose, mouth, skin, and urogenital and gastrointestinal tracts, and about four-fifths of them are beneficial to human health. Many not only facilitate proper biological activities but are essential, and they exist in a true symbiotic relationship with the human body.2 Disruption (dysbiosis) of the microbiome due to the use of antibiotics, viral infections, or stress, consequently, can lead to malfunctioning of those biological systems, resulting in disease.

When the human genome was first sequenced, it was a surprise that not all the necessary genes to support life are present. In fact, many metabolic functions are supported by the commensal microorganisms that inhabit the human body and are crucial to human health. Research efforts demonstrated many links between dysbiosis and disease. As expected, gastrointestinal disorders and allergies are connected to disruption of the microbiome, but so are many others, including cardiovascular diseases; metabolic, autoimmune, and neurological disorders; diabetes; and cancer.3 Gut microbiota not only play a role in gastrointestinal disorders, but they also influence development of the immune system4 and contribute to metabolic diseases, including obesity, insulin resistance, and type 1 and type 2 diabetes.3

The success (first U.S. FDA approval was Rebyota® in 2022) of fecal microbiota transplantation (FMT) as a treatment for Clostridioides difficile (C. diff.), a recurrent intestinal infection that was named a national health threat in the United States in 2013 by the Centers for Disease Control and Prevention (CDC), has created real interest in the potential of microbiome-based therapeutics. FMT involves treatment of patients with the microbial community of healthy donors in order to displace the dysbiotic gut microbiota and to modify the diseased gut.

FMT carries risks, however, and is not readily scalable. The alternative is to identify the organism or consortia of organisms that are contributing to resolution of the problem causing the disease. These live biotherapeutic products (LPBs) today represent a growing market with significant potential.

Researchers are not only identifying LBP candidates but also investigating methods for their delivery to the intended site from typical encapsulation to delivery platforms, such as Scioto Bioscience’s activated bacterial therapeutics (ABT). ABT enables bacteria to persist in the gut by delivery of the therapeutic bacteria in a biofilm state. Alternatively, Novome Biotechnologies’ genetically engineered microbial medicines (GEMMs) proprietary platform enables controlled engraftment for sustained and effective therapies. In addition, spore-forming bacteria provide a natural delivery mechanism, as the spore state provides stability and resistance to acidic conditions and oxygen environments.

Investment in companies developing microbiome-based therapies reached record levels in 2021. The funding paradigm shifted to more mature companies in 2022, and some developers ended up downsizing or merging to avoid closure.5 Others, however, have benefited. One example is Seres Therapeutics, which has forward movement on the back of funding from Nestlé Health Science and is waiting to hear the FDA’s decision about its Biologics License Application (BLA) for SER-109, a treatment for recurrent C. diff. infections. Nestlé also signed a licensing agreement with Enterome, and Merck is collaborating with Genome & Company on a combination therapy comprising the immuno-oncology microbiome therapeutic GEN-001 and the checkpoint inhibitor Keytruda® for the treatment of biliary tract cancer.

These are just a few of the notable deals that took place in 2022. Having such big players involved in the market instills confidence in the field. A further demonstration of belief in the field is the recent investment of €80M into Biose Industrie by L-GAM and the French State5 and the acquisition of 4D Pharma by Bacthera.6 They illustrate key trends in investment: focus on later-stage products and more money in fewer deals,7 creating consolidation.

Therapeutic Potential of Live Biotherapeutic Products

Much of the focus in the field of microbiome-based therapeutics is on gastrointestinal disorders (e.g., ulcerative colitis, Crohn’s disease, irritable bowel syndrome), diseases for which there is strong evidence of the role of the microbiome (e.g., psoriasis, autoimmune diseases), neurological diseases that involve the gut–brain axis (e.g., autism, depression), and infectious diseases (e.g., bacterial vaginosis, C. diff). Other indications with a strong association to the microbiome include infertility and improving efficacy of checkpoint inhibitors for cancer treatment.

In addition to LBPs, there are several other strategies for developing microbiome-based therapeutics.8 One involves the use of small molecule bacterial metabolites that have been shown to have an active role in inhibiting disease mechanisms. Others are developing proteins that have been shown to be produced by microbiome-derived microbiota and contribute to properly functioning biological systems. Less common is the production of engineered bacteria that behave similarly to bacteria found in the human microbiome and the use of bacteriophages — engineered viruses designed to infect bacterial cells and change their genetic code to kill off those that are undesirable or change their behavior in some way.

When it comes to LBPs, many of the first products under development were based on single strains. The work on these products is providing promising proof of concept for LBPs. That has facilitated the move to the development of consortia — sometimes composed of as many as 50 strains. The challenge has been to find methods for growing multiple strains simultaneously to facilitate scalability. Progress is being made, and ultimately consortia are likely to dominate the pipeline.

For many current candidates in clinical studies, early-phase data has been promising. Examples include the results obtained by Seres Therapeutics for SER-109 (excluding one poorly designed and recruited phase II study); Scioto Biosciences in autism spectrum disorder; Adiso Therapeutics (previously Artugen) for recurrent C. diff.; Osel for women’s health, cancer, and stem cell transplant rejection; Novome Biotechnologies for enteric hyperoxaluria; and YSOPIA Biosciences for Xlq1 in obesity. These are just a few examples. In fact, there were at least eight organizations with microbiome-based treatments for skin conditions in phase I or II clinical trials, with several in preclinical development.9 Trials are also underway in Parkinson’s disease, various gastrointestinal disorders, numerous cancers, and other indications.

Interesting areas of research that are anticipated to lead to new microbiome-based therapeutics include the tumor microbiome, particularly intratumoral fungi that impact patient responses to immunotherapy; biohybrid bacteria–based microrobots that enter solid tumors and deliver cytotoxic payloads; bacteriophages; and consortia communication via DNA messaging to enable the expression of complex behaviors.7 New and stronger evidence supporting the role of the microbiome in autoimmune diseases and the gut–brain axis and its role in depression and Parkinson’s diseases are creating additional excitement.

Many Hurdles to Overcome

While LBPs have shown great potential across many disease classes, getting from a strain or consortium that has been shown to be effective to an approved product is not a simple exercise.10–15 There are development and manufacturing challenges, a scarcity of expertise and experience with LBPs in the contract manufacturing space, regulatory issues, and safety concerns layered on top of diverse and complex patient populations and the need for more research and data.

Basic questions — such as how to grow an identified strain to a sufficiently high density and ensure colonization under practical and industrializable conditions — must be answered. For large consortia, finding a way to grow all of the strains together in a single medium — as opposed to growing each separately and then combining them — is a big hurdle for manufacturing. Selecting the right dosage, identifying the optimum time of administration, understanding the influence of the matrix, and identifying the critical protective measures (as live organisms, LBPs are typically sensitive to environmental stresses) are all important factors.10 In fact, one of the biggest challenges in LBP development is identifying the mechanism of action of these novel therapeutics.11

Developers often do not think these crucial aspects through and end up with processes and systems that are too complex, time-consuming, and expensive and thus not commercially viable. One solution is to employ an appropriate screening approach to ensure that the best strain(s) and production systems are selected upfront at the beginning of the project.

Different manufacturing challenges are associated with different types of microbes. Strict anaerobes must be maintained in an anaerobic atmosphere throughout all process steps to ensure maintenance of viability. Spore-formers must be handled in appropriate facilities designed to maintain containment and segregation between manufacturing suites. For all kinds of microbes, batch-to-batch variability is a key issue to overcome.12

Lyophilization, used to preserve the bacteria during storage and shipment, must be performed carefully to avoid negatively impacting viability and thus requires specialized expertise. Waking up those lyophilized bacteria is a strain-dependent problem that delivery technologies may ultimately help overcome. The issue is even more complicated for consortia, as the behavior of individual strains in this context may be quite different. In all cases, successful introduction of these organisms to the microbiome requires overcoming homeostatic mechanisms designed to resist change.

Developers are also faced with finding outsourcing partners with experience and expertise in the development and manufacture of LBPs from preclinical to commercial stages. Most CDMOs have limited expertise with LBPs and struggle to maintain viability of the microorganism throughout the entire manufacturing process, a critical component to success. Most startup companies have not progressed beyond the bench scale and typically require development of a scalable process, media, and formulation. Critical elements include optimization of the cultivation, timing, and atmosphere maintained during the harvest, as well as formulation combined with the lyophilization cycle. Most also lack knowledge of how to establish the qualified analytical assays necessary for testing of LBPs. Access to a CDMO like List Labs that can provide comprehensive support from early- to late-phase clinical development through commercial launch and post-marketing approval saves developers costs and time.

There are regulatory uncertainties as well, including the lack of a universally accepted definition or classification system, a well-defined approval pathway, and robust clinical data to support claims. In the United States, the FDA defines an LBP as a biological product that: (1) contains live organisms, such as bacteria; (2) is applicable to the prevention, treatment, or cure of a disease or condition of human beings; and (3) is not a vaccine and has published guidance for developers.16 The European Medicines Agency, meanwhile, considers LBPs to be another class of biologics and has not established any separate approval pathway.17 Both agencies have, however, issued guidance on the use of spore-forming microorganisms for drug manufacture.18,19

As candidates have progressed from R&D to clinical development and the submission of investigational new drug (IND) applications, industry and regulatory bodies are both learning more about what future expectations will be with regard to required chemistry, manufacturing, and control (CMC) data and other information that will be considered essential for ensuring the safety, quality, and efficacy of LBPs.20,21

Concerns about the safety of FMT are real and must be addressed. Issues have arisen with FMT therapies that have brought attention to the possible safety issues with treatments based on donor-derived products. Fecal transplants are different than LBPs based on cultivated bacteria, as they may carry donor microorganisms that can cause infections in the recipient. However, LBP products manufactured through a controlled fermentation process provide a greater level of assurance, since the purity of the product can be strictly maintained.

Some challenges include the fact that LBPs do not enter the systemic circulation, so toxicity may not be related to dosage, and the inability to use animal models to generate data, given that LBPs are designed specifically based on the human microbiome.21 In addition to antimicrobial resistance genes, other attributes of LBPs can affect safety and must be carefully evaluated, including virulence factors, translocation ability, metabolic activities, and potential drug–drug interactions.22 These and other issues make the use of risk-based safety assessments essential.

Product performance can depend on the environment within individual patients and the content of each person’s microbiome,12,13 making it difficult to demonstrate efficacy and predict pharmacokinetics, which adds to regulatory uncertainty. It can be challenging in preclinical development to design non-clinical studies that account for host-specific attributes that can impact efficacy and safety.

Finally, there is still much in the microbiome field that remains unknown. More knowledge of the role of the microbiome in health and disease is needed, as is a greater understanding of the complexity and functions of microbial communities.13

Outlook for the LBP Sector

The nascent nature of the LBP market, combined with initial promising results coming out of a myriad of early clinical trials, presents an exciting picture with respect to the sector’s potential for growth. Our limited understanding of the disease mechanisms involving the microbiome suggests that the indications for which LBPs can be effective will only expand in number. Many, in fact, believe LBPs could revolutionize medicine and the way patients are treated in the future.

Increasing our knowledge of the microbiome and its role in health and disease must remain primary goals. Fit-for-purpose manufacturing, analytical, and delivery solutions are also needed. Methods for efficiently growing consortia and determining appropriate dosing levels will be crucial for further advances in the field, as well as finding ways to manage patient diversity and its impact on LBP performance. Clarification of regulatory guidance and establishment of a global, common approval pathway will go a long way toward assuring success of LBPs. To address these issues, continued research and collaboration is paramount among the industry, regulatory agencies, and scientific communities. Along those lines, the work that must still be done should be parsed sensibly between academia, drug developers, and CDMOs. For CDMOs, key roles will involve resolving challenges in manufacturing, formulation, delivery, and storage.

Efforts directed toward overcoming these challenges are currently driven by excitement around the potential of LBPs. Once the first approval of an LBP is realized in the United States and Europe, the market will be truly energized. We have already seen the first FMT approval, which has been positive for the market. Phase III successes with LBPs will also make a difference. As more pre-IND meetings take place with the FDA and regulatory expectations become clearer, companies will continue to devise ways to meet the challenges created by those requirements.

This evolving process will continue to move the field forward, and five years from now there should be at least one approved and commercialized LBP product on the market and a couple more on the cusp of being launched. Consequently, there will be much greater traction in the field, with numerous approvals following soon after, and not just products targeting gastrointestinal diseases but products designed to treat a wide range of indications, including neurodegenerative disorders and various types of cancer. It is also likely that injectable products containing LBPs directed towards tumors or other specific sites — more in line with immunotherapies or vaccines — will be in development and advancing toward commercialization.

Technologies, such as microrobots, injectable spores, and self-assembling protective coatings,23 are just the tip of the iceberg with respect to new technologies and approaches for engineering organisms and how they are delivered. Leveraging the unique mechanisms of action of LBPs in combination therapies with conventional drugs will also become more prevalent as the impact of microbiome-based therapeutics on the body’s response to different treatments becomes better understood.

In terms of value, various market research firms have the global LBP market expanding at a double-digit compound annual growth rate (CAGR) ranging from 36%24 to 47.5%25 to 54.8%.26 The value of the microbiome-based therapeutics market, including FMTs, LBPs, postbiotics, prebiotics, phages, and antimicrobials, is estimated to reach $1.5 billion by 2027.26

As of December 2022, approximately 200 companies, mostly startups, were developing microbiome-based therapies, many with funding support from Big Pharma firms.25 Most projects were at the preclinical stage, but approximately 15 were in phase II/III clinical trials. As of April 2022, over 140 clinical trials involving microbiome-based therapeutics had been registered worldwide, with the number increasing at a CAGR of 26% from 2016 to 2021. At the time, 49% of the studies were active and recruiting patients, and 36% had been completed.24 At that time, more than 25 CDMOs were offering LBP development and production services, and more than 35 production facilities dedicated to microbiome-based therapies had been established (nearly 60% in Europe). Of companies pursuing in-house manufacturing, over half were located in North America.

Focused Support from List Labs / List Bio

Soon after its founding in 1978, List Labs established a leadership position in the toxin industry and became a reliable supplier of quality reagent-grade bacterial products and toxins, including botulinum toxins. A collaboration with a large commercial manufacturer of botulinum toxin helped the company build extensive knowledge about the design and process requirements for optimal GMP manufacture of these types of organisms.

In its first state-of-the-art GMP manufacturing facility expertly designed for up to Biosafety Level (BSL) 3 organisms and spore formers, List Labs has worked with more than 60 different species of microorganisms and hundreds of different strains, including anaerobes, aerobes, and spore formers, comprising difficult-to-grow organisms from the phyla Bacteroides, Firmicutes, Verrucomicrobia, and Actinobacteria. The natural next step in the company’s evolution was to offer this experience and expertise to developers of microbiome-derived therapeutics, particularly LBPs. In fact, List Labs was one of the first companies to manufacture an LBP that progressed into clinical trials and is now poised for phase III trials.

The San Jose, California, clinical-scale facility is equipped with stainless-steel reactors up to 100-L working volume, a new 500-L single-use stirred-tank reactor, and systems for sterile fill/finish, the filling of vaginal applicators and powders into vials, and small-scale manual filling of capsules. It was carefully designed to minimize the risk of cross-contamination and maintain segregation, even for spore-forming organisms.

In response to requests from customers to expand its capabilities to include large-scale manufacturing of LBPs in support of their upcoming phase III studies and future commercial product launches, List Labs welcomed the acquisition of 60% of the company by South Korean drug developer Genome & Company in 2021, which came with a commitment to construct a large-scale CDMO facility under the auspices of new sister company, List Bio.

The new facility, which is located in Indiana, will include upstream and downstream processing for drug substance manufacturing, as well as all ancillary operations required to support GMP manufacturing. Single-use equipment will be installed, as well as capability for lyophilization. Advanced containment and segregation technology similar to that installed in the California facility is being deployed, for production of aerobic, anaerobic, and spore-forming organisms through fill and lyophilization. Encapsulation capabilities may also be added in the future if warranted by specific projects.

The groundbreaking ceremony for the List Bio facility in Indiana was held on June 8, 2022. The goal is to have the site completed by the end of 2024, with GMP production initiated in early 2025. List Labs and List Bio are working collaboratively and have aligned their basic processes, procedures, and management and quality systems. List Labs and List Bio intend to merge to establish an end-to-end service provider in the microbiome and live bacterial manufacturing space supporting projects seamlessly from preclinical studies to clinical development and all the way through phase III and commercial launch.

Over the last several decades, List Labs has amassed a broad array of expertise in the development and manufacture of all types of organisms, maintaining the viability of both aerobic and anerobic organisms throughout the entire manufacturing process and safely handling spore formers in segregated environments, along with expertise in purification of bacterially expressed proteins. Our origins as a producer of quality reagent-grade materials for the research market has instilled a scientific yet flexible mindset grounded in openness and transparency, a passion for bringing these novel therapeutics to patients, and a willingness to go beyond expectations to offer the highest-quality products, solve problems, develop innovative solutions, and continuously improve.

The relationship List Labs has with Genome & Company is another advantage for customers. With its pipeline of LBP products, Genome & Company brings additional expertise of its own as well as that of the leading pharmaceutical companies with which it collaborates. Combined with our ability to provide end-to-end solutions for not just LBPs but many types of microbiome-based therapeutics, List Labs is very well positioned to facilitate the tremendous growth trajectory of this exciting new field that will improve patient lives and perhaps lead to fundamental changes in the practice of medicine.



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Stacy Burns-Guydish, Ph.D.

With over 25 years’ experience in transformative biotechnology applications for microbes, Dr. Burns-Guydish has developed breakthrough technologies for bacterial production of a biochemical resulting in intellectual property and patents and scaled up a strict anaerobic fermentation to 100,000 L. Joining List Labs in 2016, she has directed the development and manufacturing of many different live biotherapeutic drug products for phase I and II clinical trials. Dr. Burns-Guydish earned her Ph.D. in microbiology and immunology from Baylor College of Medicine and completed her postdoctoral training at Stanford University School of Medicine.