Understanding the Importance of Microbiome Research
The human microbiome, composed of trillions of microorganisms, plays a fundamental role in health and disease. These microbes influence digestion, immune response, metabolism, and even neurological functions. Research in this field has advanced significantly, revealing connections between microbiome imbalances and conditions such as obesity, diabetes, inflammatory disorders, and neurodegenerative diseases.
Microbiome research is also central to the development of personalized medicine. By analyzing individual microbiome compositions, scientists can tailor therapies to improve treatment outcomes. The growing awareness of the microbiome’s impact has fueled investment in diagnostics, therapeutics, and nutrition-based interventions.
The Microbiome Market Outlook
The global human microbiome market has experienced rapid growth, with projections estimating it will reach approximately USD 4.9 billion by 2031, growing at a CAGR of 24.5%. This expansion is driven by increased demand for microbiome-based treatments, advances in sequencing technologies, and a deeper understanding of microbial functions in health and disease.
Leading US-Based Microbiome Companies (2025)
The following companies are at the forefront of microbiome research and applications in healthcare, developing innovative solutions to improve human health.
Axial Biotherapeutics (Waltham, MA)
Axial Biotherapeutics focuses on developing microbiome-inspired therapeutics for neurological disorders. Their research centers around the gut-brain axis, investigating how gut microbiota interact with the central nervous system. The company’s lead programs target conditions such as autism spectrum disorder (ASD) and Parkinson’s disease. Axial employs a proprietary drug discovery platform that identifies microbial metabolites affecting neurological pathways, paving the way for novel therapeutic interventions.
BiomeSense specializes in microbiome data collection and analysis through its biosensor platform. Their core technology allows for real-time, continuous microbiome monitoring, providing a comprehensive picture of microbiome fluctuations over time. This approach is particularly beneficial for clinical trials and long-term health monitoring. BiomeSense collaborates with pharmaceutical companies and academic researchers to enhance microbiome-related drug development and diagnostics.
ResBiotic develops probiotic-based solutions to improve respiratory health. Their flagship product, ResB Lung Support, is a clinically validated probiotic formula designed to support lung microbiome balance and reduce inflammation. The company is actively expanding its research pipeline, exploring probiotics for conditions like chronic obstructive pulmonary disease (COPD) and asthma. By leveraging microbial strains with anti-inflammatory properties, ResBiotic aims to offer safe and effective respiratory health solutions.
Finch Therapeutics (Somerville, MA)
Finch Therapeutics is a leader in microbiome-based therapeutics, particularly for gastrointestinal diseases. The company’s Full-Spectrum Microbiota (FSM) platform utilizes diverse microbial communities from healthy donors to restore gut microbiome balance. Their leading drug candidate, CP101, is in advanced clinical trials for recurrent C. difficile infection. Finch is also investigating microbiome therapeutics for inflammatory bowel disease (IBD) and other gut-related disorders, aiming to harness the power of the microbiome to treat chronic conditions.
Viome offers at-home microbiome testing services using RNA sequencing and artificial intelligence to analyze gut, oral, and cellular health. Their proprietary AI-driven platform translates microbiome data into personalized dietary and lifestyle recommendations. Viome has also expanded into diagnostics, developing early-stage tests for chronic diseases, including cancer and metabolic disorders. Their mission is to enable precision health through microbiome-driven insights, helping individuals optimize their well-being.
Second Genome (South San Francisco, CA)
Second Genome utilizes a proprietary drug discovery platform to analyze microbiome-derived proteins and peptides for therapeutic applications. Their research focuses on identifying microbial signals that modulate immune responses, with applications in inflammatory diseases, metabolic disorders, and oncology. Second Genome collaborates with leading biotech firms and research institutions to develop microbiome-based drug candidates, particularly in immuno-oncology, where the gut microbiome plays a crucial role in patient response to cancer treatments.
Persephone Biosciences (San Diego, CA)
Persephone Biosciences applies artificial intelligence and synthetic biology to microbiome research, with a focus on immuno-oncology. The company’s research aims to identify beneficial microbes that influence immune function in cancer patients. Persephone’s ongoing clinical studies analyze gut microbiome profiles in individuals undergoing immunotherapy, helping develop precision medicines that enhance treatment efficacy. Their work bridges the gap between microbiome science and oncology, offering new pathways for personalized cancer care.
Sun Genomics provides customized probiotics based on individual gut microbiome analysis. Their flagship product, Floré, utilizes whole-genome sequencing to create tailored probiotic formulations that address specific gut health needs. Customers receive in-depth gut microbiome reports and personalized probiotic blends designed to optimize digestion, immunity, and overall well-being. Sun Genomics continues to expand its research into microbiome-targeted interventions for various health conditions, including gastrointestinal disorders and metabolic syndromes.
Microgenesis specializes in reproductive health, offering diagnostic tools to detect microbiome imbalances that may contribute to infertility. Their proprietary test evaluates vaginal and intestinal microbiota, identifying potential disruptions linked to inflammation and reproductive challenges. Microgenesis also provides personalized microbiome-based interventions to support fertility treatments. Their research aims to improve fertility outcomes by restoring microbial balance, addressing an often-overlooked factor in reproductive medicine.
AnimalBiome focuses on microbiome health in pets. Their diagnostic tests analyze gut microbiota composition in cats and dogs, identifying imbalances that may contribute to digestive disorders, skin conditions, and immune dysfunction. The company offers personalized microbiome restoration supplements to improve pet health, leveraging data-driven insights to enhance veterinary care. AnimalBiome collaborates with research institutions to advance understanding of the pet microbiome and its role in overall animal wellness.
BrickBuilt Therapeutics (Allston, MA)
BrickBuilt Therapeutics is a microbiome biotechnology company focused on developing Live Biotherapeutic Products (LBPs) for oral health. Their research targets oral dysbiosis, aiming to eliminate harmful pathogens while promoting beneficial microbial communities in the mouth. The company is currently engaged in preclinical studies evaluating microbial strains for their ability to prevent periodontal disease and combat halitosis. Collaborations with microbiome laboratories and dental research institutions are central to their development efforts.
A subsidiary of Ferring Pharmaceuticals, Rebiotix is a microbiome company that specializes in microbiota-based therapeutics. Their FDA-approved product, RBX2660, is an innovative therapy that prevents recurrent Clostridioides difficile (C. diff) infections by restoring gut microbial balance. The company is expanding its microbiome biotechnology pipeline to target conditions like inflammatory bowel disease (IBD) and antimicrobial resistance, leveraging extensive clinical trial data to develop next-generation microbiome therapies.
Oralta is a microbiome company pioneering probiotic-based solutions for oral health. Their probiotic blends are formulated to combat bad breath by enhancing the oral microbiome’s natural balance, reducing odor-causing bacteria. The company collaborates with leading microbiome laboratories to validate its formulations through clinical studies and is investigating additional applications in periodontal health and cavity prevention.
Siolta Therapeutics (San Francisco, CA)
Siolta Therapeutics is a clinical-stage microbiome biotechnology company focused on developing microbiome-based treatments for inflammatory diseases. Their lead candidate, STMC-103H, is in clinical trials for preventing allergic diseases, particularly asthma, by modulating the gut microbiome. Siolta is also researching interventions for early-life immune development, working with microbiome laboratories to optimize microbial consortia for therapeutic applications.
Nexilico is a microbiome company that integrates computational biology and artificial intelligence to accelerate microbiome-targeted drug discovery. Their proprietary AI platform models microbial interactions in the human body, helping predict how microbiome modulation can influence drug metabolism. Nexilico collaborates with pharmaceutical partners and microbiome laboratories to identify new therapeutic candidates, focusing on precision medicine applications.
Seres Therapeutics (Cambridge, MA)
Seres Therapeutics is a leading microbiome biotechnology company that develops microbiome therapeutics. Their flagship product, Vowst (formerly SER-109), received FDA approval in April 2023 as the first oral microbiome therapeutic for preventing recurrent C. difficile infections. Seres continues expanding its research into conditions like ulcerative colitis and antimicrobial resistance. Their partnerships with microbiome laboratories help refine the bioprocessing and formulation of their microbial consortia therapies.
Scioto Biosciences (Indianapolis, IN)
Scioto Biosciences is a microbiome company developing live bacterial therapeutics using its proprietary Activated Bacterial Therapeutics (ABT) platform. Their lead candidate, SB-121, is in preclinical trials for treating necrotizing enterocolitis, a severe gastrointestinal disease affecting premature infants. The company is optimizing bacterial biofilm-based delivery systems to enhance microbial colonization and therapeutic efficacy. Scioto collaborates with microbiome laboratories to expand its research into additional indications.
Azitra is a microbiome biotechnology company developing microbiome-based therapies for skin diseases. Their lead candidate, ATR-12, is in clinical development for treating Netherton syndrome, a rare genetic skin disorder. Azitra’s research explores engineered commensal bacteria capable of producing therapeutic proteins that restore skin barrier function. Their pipeline also includes potential treatments for eczema and ichthyosis vulgaris, developed in partnership with microbiome laboratories specializing in dermatology.
Vedanta Biosciences (Cambridge, MA)
Vedanta Biosciences is a microbiome company pioneering microbiome-derived immunotherapies. Their lead candidate, VE303, is in clinical trials for preventing recurrent C. difficile infections. Vedanta is also developing microbiome-based treatments for inflammatory bowel disease (IBD) and cancer immunotherapy by leveraging rationally designed microbial consortia. The company collaborates with microbiome laboratories to ensure rigorous preclinical and clinical validation.
Kanvas Biosciences (Princeton, NJ)
Kanvas Biosciences is a microbiome biotechnology company specializing in the discovery, development, and manufacturing of microbiome-based therapeutics. The company has developed a novel spatial biology platform that can profile host-microbe interactions, providing insights into the microbiome's role in health and disease. In October 2023, Kanvas Biosciences expanded its capabilities by acquiring assets from Federation Bio, including two active clinical programs, a microbial library, and intellectual property. This acquisition accelerates their immuno-oncology program in collaboration with The University of Texas MD Anderson Cancer Center, aiming to enhance patient responses to immunotherapy. Additionally, Kanvas is advancing a program targeting inflammatory bowel disease, leveraging their expertise in engineering complex microbial consortia. The company operates facilities in both Princeton, NJ, and South San Francisco, CA, focusing on the development and manufacturing of live biotherapeutic products.
Conclusion
Microbiome research continues to drive groundbreaking discoveries, reshaping our understanding of human health and disease. The microbiome biotechnology industry is advancing rapidly, with companies developing innovative therapies, precision diagnostics, and targeted interventions for conditions ranging from gastrointestinal disorders to neurological and metabolic diseases.
With the market projected to grow significantly in the coming years, microbiome companies are playing a crucial role in translating research into real-world applications. From microbiome laboratories pioneering new therapeutic pathways to digital solutions like Scispot enabling more efficient data management and workflow automation, the field is evolving at an unprecedented pace.
As investment and scientific breakthroughs accelerate, the future of microbiome-based healthcare looks promising. Whether through probiotics, live biotherapeutics, AI-driven microbiome analysis, or next-generation sequencing, microbiome research is poised to transform medicine, paving the way for more personalized, effective, and sustainable treatments.
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