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Recent advancements in microbiome research have ushered in a new era of medical opportunities, highlighting the transformative potential of microbiome-based therapies. Leveraging advanced genome sequencing techniques, researchers now possess a deeper understanding of microbiome structure and function, allowing for precise identification of the diverse roles microbes play in health and disease, paving the way for innovative treatments.
The development of microbiome-based therapeutics is rapidly expanding, with significant interest in using probiotics, fecal transplantation, phage therapy (BiomX) and other microbiome-modulating approaches to address various diseases. Others like Bloom Science are developing a platform approach with their IrisRx™ platform that was developed utilizing a reverse engineering method leveraging the crucial communication between the gut – brain axis.
Technological advancements in sequencing, such as those developed and offered by QIAGEN, have enabled high-resolution analyses at the species or strain level, facilitating precise characterization of microbiome changes and their impacts. Additionally, improved culturing techniques and the integration of multi-omics data are providing deeper insights into microbiome function and host-microbe interactions. These breakthroughs are not only enhancing our understanding but also driving the development of targeted, effective microbiome-based diagnostics and therapeutics, offering new hope for patients across various medical fields.
Let’s explore some of the most promising microbiome-based approaches to new therapies and drugs that are both FDA approved and currently in development.
Clostridioides difficile infection (CDI)
Several FDA approved therapies exist for Clostridioides difficile infection (CDI), such as Ferring Pharmaceuticals’ Rebyota was the first FDA-approved microbiome-based therapeutic for recurrent CDI. Also, Seres Therapeutics, Vowst™, co-developed by Nestle Health Sciences, received FDA approval in April 2023 for the orally administered spore-based medication designed to prevent CDI recurrence.
Other Live Biotherapeutic Products (LBPs) are in development by Vedanta Biosciences who is using an oral bacterial consortium candidate consisting of eight types of non-toxic, non-pathogenic, commensal strains of Clostridia, and Finch Therapeutics who is developing an oral FMT product administered as one-dose capsules (development was halted).
Phage Therapy
Phage therapy involves using bacteriophages to target and eliminate specific pathogenic bacteria in the microbiome. Phage therapy is emerging as a promising microbiome-based approach to precisely target and eliminate specific pathogenic bacteria without disturbing the entire microbial ecosystem.
BiomX, is a leader in this space, headquartered in Ness Ziona, Israel, and having recently acquired Maryland-based Adaptive Phage Therapeutics (APT). The company is focused on developing natural and engineered phage cocktails designed to target and destroy harmful bacteria in the treatment of chronic diseases. Their approach involves discovering and validating proprietary bacterial targets and customizing phage compositions against these targets. APT’s Phage Bank library of systematically discovered, selected, cataloged, and curated phages further enhanced BiomX’s IP and technology enabling for the personalization of custom phage treatments based on specific bacterial strains isolated from patients, enhancing the precision and effectiveness of the therapy.
Locus Biosciences, located in Morrisville, NC, combines CRISPR-Cas3 technology with bacteriophages to develop CRISPR-engineered bacteriophage therapeutics. This approach allows for precise targeting and eradication of harmful bacteria within the microbiome, potentially offering a significant advantage over broad-spectrum antibiotics.
Telum Therapeutics, based in Noáin, Spain, is dedicated to developing bacteriophage therapies for microbiome applications, though detailed information on their specific targets remains limited. These companies exemplify the innovative strides being made in phage therapy, which holds great potential for treating infections with high precision and minimal disruption to the beneficial microbial communities.
Treatments for CNS
Recent advancements in microbiome research are opening up promising new avenues for treating central nervous system (CNS) disorders. Bloom Science is at the forefront of developing microbiome-based therapeutics for neurological diseases through their innovative IrisRx™ platform. This cutting-edge approach focuses on the gut-brain axis, leveraging the crucial communication between the gut microbiome and the central nervous system. By utilizing a reverse engineering method, Bloom Science starts with responder data to develop novel microbiota drug candidates. Their proprietary platform creates multi-functional therapeutics from gut commensal microbes, advancing synthetic biology to engineer beneficial bacterial consortia and strains found in the gut’s mucosal layer.
Bloom Science targets several challenging neurological conditions, including Dravet syndrome and other rare epilepsies, Amyotrophic Lateral Sclerosis (ALS), autism, Parkinson’s disease, and Alzheimer’s disease. Their lead program, BL-001, is an orally-administered Live Biotherapeutic Product (LBP) designed to mimic the antiepileptic effects of the Ketogenic Diet for treating Dravet syndrome and other rare developmental and epileptic encephalopathies (DEEs). Another promising candidate, BL-002, is in development for ALS.
Treatments for neurological conditions are being developed by MaaT Pharma who is in a Phase Ib trial for amyotrophic lateral sclerosis (ALS). 4D Pharma is developing live biotherapeutic products using their MicroRx platform that show potential for Parkinson’s disease. NuBiyota is testing their microbial ecosystem therapeutic technology-based product MET-2 for anxiety and depression. Finch Therapeutics is also developing FIN-211 for targeting gastrointestinal complications in autism spectrum disorder (ASD).
Innovative therapies are being developed that leverage the intricate relationship between the gut microbiome and brain function. Additionally, postbiotics, which are metabolites produced by gut bacteria, such as short-chain fatty acids, are being studied for their neuroprotective effects. These therapies offer a novel approach to addressing CNS disorders by targeting the root causes rather than just symptoms.
Understanding the gut-brain axis is crucial for these advancements. This complex communication network involves neural, immune, metabolic, and endocrine pathways that link the gut and the brain. The vagus nerve, immune system modulation, microbial metabolites, and stress regulation pathways all play a role in how gut bacteria influence brain health. These discoveries highlight the potential for microbiome research to revolutionize our understanding and treatment of brain health.
Oncology
Companies such as Vedanta Biosciences are advancing the field with their rationally defined consortia of human microbiome-derived bacteria, focusing on identifying commensal bacteria that induce immune responses crucial for cancer immunotherapy.
4D Pharma is another key player, developing live biotherapeutic products (LBPs) for cancer treatment. In partnership with Merck, they are exploring the potential of combining LBPs with KEYTRUDA® (pembrolizumab) to treat solid tumors. Seres Therapeutics is focused on developing microbiome therapeutics to enhance the efficacy of cancer immunotherapies, particularly checkpoint inhibitors. MaaT Pharma is developing microbiome therapies for cancer patients. Additionally, MRM Health is working on differentiated microbiome consortia therapeutics for various diseases, including cancer. Their platform aims to develop treatments that leverage the microbiome’s role in modulating the immune system.
These companies exemplify the innovative approaches being pursued to harness the power of the microbiome in the fight against cancer, offering new hope and improved outcomes for patients.
Gastrointestinal and Infectious Disease Therapies
These areas show particular promise for microbiome-based drugs, likely due to the more advanced state of microbiome science in these fields. Several pioneering companies at the forefront of developing treatments for gastrointestinal and infectious diseases.
Seres Therapeutics has made significant strides with Vowst™ (SER-109), an FDA-approved oral medication co-developed with Nestlé Health Sciences to prevent recurrent Clostridioides difficile infection (CDI). Vowst™ works by restoring the gut microbiome with beneficial Firmicutes bacteria. Similarly, Ferring Pharmaceuticals has developed Rebyota, the first FDA-approved fecal microbiota transplantation (FMT) therapy for recurrent CDI, administered via enema and containing a diverse consortium of live microbes from human stool.
Vedanta Biosciences is another key player, targeting CDI, inflammatory bowel disease (IBD), and food allergies with its defined bacterial consortia aimed at modulating the gut microbiome. Enterome leverages its Mimicry biocomputational platform to identify gut bacteria-derived peptides and proteins for treating cancer and immune diseases, while also developing EndoMimics, oral drugs based on proteins secreted by gut bacteria for conditions like IBD and food allergies. Infant Bacterial Therapeutics (IBT) focuses on necrotizing enterocolitis in infants, a severe gastrointestinal infection. Mikrobiomik is developing therapies for various gastrointestinal conditions, including IBD and CDI, while Kaleido Biosciences is working on microbiome metabolic therapies (MMTs) targeting gut microbiome to treat a range of diseases. Lastly, 4D Pharma is creating live biotherapeutic products for gastrointestinal diseases, utilizing specific bacterial strains to enhance gut microbiome health.
Other advancements in this field are being driven by an increased focus on the microbiome and strategic partnerships that are helping to develop better tools and technologies for understanding the microbiome. QIAGEN and Penn State have launched a pioneering collaboration to further microbiome research and its therapeutic applications. In January 2024, they announced the creation of a shared research and education facility at the One Health Microbiome Center (OHMC) within Penn State’s Huck Institutes of the Life Sciences. This partnership aims to address current challenges and knowledge gaps in microbiome science by studying diverse microbial communities in various environments, including the human body. The collaboration provides QIAGEN with an innovation center to develop and test new products and offers emerging researchers opportunities through internships, promoting advancements in microbiome-based therapeutics and human health.
The microbiome field of research and discovery is no small matter and will continue to advance thanks to these committed companies and pioneers in the field.
