What are the leading microbiome companies?

This blog post has been written by the person who has mapped the microbiome market in a clean and beautiful presentation

The microbiome industry has reached an inflection point in 2025, with over $1.55 billion in disclosed funding flowing to companies developing everything from live biotherapeutic products to agricultural microbiome solutions.

This sector encompasses therapeutic applications targeting inflammatory bowel disease and infection prevention, diagnostic platforms using spatial mapping technologies, and consumer products ranging from engineered probiotics to skin microbiome ingredients.

And if you need to understand this market in 30 minutes with the latest information, you can download our quick market pitch.

Who are the top microbiome companies in 2025 by revenue, funding, or scientific breakthroughs?

Indigo Agriculture dominates the funding landscape with a massive $1.2 billion Series G round, though their focus on agricultural microbiome applications differs from human health players.

In the human therapeutics space, Microbiotica leads with £50 million ($67 million) Series B funding for precision live bacterial therapeutics targeting immuno-oncology and inflammatory bowel disease. EnteroBiotix secured £27 million ($34 million) in grant funding from the Bill & Melinda Gates Foundation for defined consortia treating liver pathologies.

Seres Therapeutics achieved a critical revenue milestone by selling their FDA-approved VOWST™ therapy for $155 million, marking the first major commercial success in microbiome therapeutics. Their SER-155 demonstrated 77% reduction in bloodstream infection risk in clinical trials. Vedanta Biosciences generated $33.8 million in revenue while advancing VE303 through successful Phase 2 trials for recurrent C. difficile infection.

MaaT Pharma secured €35 million from the European Innovation Council for their Phase III MaaT013 program, which showed 44% one-year survival rates in graft-versus-host disease patients. Synlogic's $30 million partnership with Roche validates their engineered probiotics platform for inflammatory bowel disease and phenylketonuria.

Need a clear, elegant overview of a market? Browse our structured slide decks for a quick, visual deep dive.

Which microbiome startups raised the most funding in 2024 and 2025, and how much did they receive?

Beyond Indigo Agriculture's agricultural focus, Microbiotica's £50 million Series B represents the largest human health microbiome funding round in this period.

If you want fresh and clear data on this market, you can download our latest market pitch deck here

Who are the major investors backing these companies, and what amounts have they committed?

The Bill & Melinda Gates Foundation emerges as the most active grant provider, committing over $50 million across EnteroBiotix, Siolta Therapeutics, and Freya Biosciences for infectious disease and women's health applications.

ARPA-H and CARB-X represent significant government funding sources, with $6.2 million to Ancilia Biosciences and Neobe, plus $3.9 million to Vedanta's VE707 program for multidrug-resistant organism prevention. Corporate venture capital arms are increasingly active, with J&J Innovation co-leading Holobiome's $9 million round and Merck Ventures participating in Kanvas Biosciences' $12.5 million Series A.

Unilever Ventures backs both Holobiome and personal-care microbiome ingredient development, reflecting their strategic interest in consumer applications. Tencent's participation in Microbiotica's £50 million round represents the largest tech company investment in microbiome therapeutics. Flagship Pioneering continues supporting Indigo Agriculture's agricultural microbiome platform with their $1.2 billion commitment.

Traditional venture capital firms like DCVC focus on platform technologies, evidenced by their investment in Kanvas Biosciences' spatial mapping capabilities. European funding sources, particularly the European Innovation Council's €20 million grant to SNIPR Biome, demonstrate strong regional support for antimicrobial resistance solutions.

Which companies received awards, recognitions, or government grants in 2024-2025?

Government and foundation grants total over $100 million across multiple therapeutic areas, with the Biocodex Microbiota Foundation providing $50,000 grants to early-career researchers studying gut-systemic interactions.

• Biocodex Microbiota Foundation (2025): Multiple $50,000 grants for gut-body axis research to early-career investigators
• Weston Family Proof-of-Principle (2024-25): Up to $300,000 per project for 16 high-risk translational microbiome biomarker discovery teams
• Danone Gut Microbiome Fellowship: $25,000 grants for graduate students researching yogurt, probiotics, and gut health interactions
• Nature-Yakult Global Grants (2025): Up to $100,000 for three projects studying nutrition-microbiome-barrier relationships
• European Innovation Council: €20 million grant to SNIPR Biome for phage-based antimicrobial development

Wondering who's shaping this fast-moving industry? Our slides map out the top players and challengers in seconds.

Which companies are developing the most promising microbiome-based therapeutics, diagnostics, or consumer products?

Live biotherapeutic products dominate the therapeutic pipeline, capturing 60% of total funding with single-strain and defined consortia targeting gastrointestinal, metabolic, and oncological indications.

Microbiotica's precision bacterial therapeutics platform targets immuno-oncology applications using patient-specific microbiome signatures. Their MB097 and MB310 candidates represent next-generation precision consortia derived from responder microbiome profiles. Vedanta Biosciences' VE303 achieved Phase 2 success in recurrent C. difficile infection, while their VE707 program targets multidrug-resistant organism prevention with CARB-X funding.

Engineered probiotics represent a growing category, with Z-Biotics developing synthetic consumer probiotics and Ancilia Biosciences advancing CRISPR-based bacterial vehicle therapies. Kanvas Biosciences' spatial microbiome mapping platform uses artificial intelligence for drug discovery applications, representing a shift toward platform-based approaches.

SNIPR Biome's phage-based antimicrobials target antibiotic resistance through precise bacteriophage cocktails. Diagnostic applications include microbiome signature biomarkers through Genentech collaborations and the University of Chicago's GB-0001 diagnostic platform. Consumer applications expand through Z-Biotics' synthetic probiotics and Freya Biosciences' vaginal microbiome immunotherapies.

Are large pharmaceutical, biotech, or food industry players partnering with or acquiring microbiome startups?

Danone's 2025 acquisition of The Akkermansia Company for an undisclosed sum signals increasing consolidation, particularly around novel probiotic strains like Akkermansia muciniphila's MucT™ for metabolic health applications.

The formation of Cmbio through the merger of Clinical Microbiomics, CosmosID, MS-Omics, DNASense, and Microba Research Services creates a unified microbiome services platform, indicating industry maturation. Genentech's partnership with Microbiotica, potentially worth up to $534 million in milestones, focuses on inflammatory bowel disease biomarkers and live biotherapeutic products.

L'Oréal invested €35 million in Abolis Biotechnologies for skin-microbiome ingredient development, reflecting cosmetics industry interest. Unilever and PepsiCo maintain research partnerships for skin and nutrition microbiome applications respectively. Roche's $30 million partnership with Synlogic validates engineered probiotics for inflammatory bowel disease and phenylketonuria treatments.

These partnerships typically involve milestone-based payments, with pharmaceutical companies providing clinical development expertise while startups contribute microbiome platform technologies. The trend toward strategic partnerships over outright acquisitions allows both parties to maintain flexibility while sharing development risks.

If you need to-the-point data on this market, you can download our latest market pitch deck here

What are the most promising technologies in microbiome R&D in 2025, and what breakthroughs are expected in 2026?

Precision consortia development leads technological advancement, with custom live biotherapeutic products derived from patient-response microbiome signatures representing the next generation of personalized medicine.

Single-cell and spatial omics technologies provide enhanced understanding of gut niches and host-microbe interactions, enabling more targeted therapeutic development. Artificial intelligence-driven research and development uses predictive modeling to optimize microbiome engineering outcomes, reducing development timelines from years to months.

Phage therapies advance through bacteriophage cocktails designed for targeted pathogen eradication, addressing antibiotic resistance challenges. The expansion beyond gut-brain axis research to include gut-lung, gut-skin, and gut-bladder axes opens new therapeutic categories. CRISPR-based bacterial vehicle therapies enable precise genetic modifications for therapeutic delivery.

Expected 2026 breakthroughs include regulatory approval for additional live biotherapeutic products beyond VOWST™, advancement of precision consortia into Phase 3 trials, and commercial launches of engineered probiotic consumer products. Spatial microbiome mapping platforms should demonstrate drug discovery applications, while phage-based antimicrobials may enter human clinical trials.

Looking for the latest market trends? We break them down in sharp, digestible presentations you can skim or share.

How is the geographic distribution of leading microbiome companies evolving?

North America dominates with approximately 60% of disclosed funding, concentrated in Boston, San Francisco Bay Area, and San Diego biotechnology hubs.

Europe captures approximately 30% of funding, with the United Kingdom leading through Innovate UK grants and large Series B rounds like Microbiotica's £50 million. Denmark and France contribute through companies like SNIPR Biome and MaaT Pharma respectively. Asia-Pacific remains a smaller market with less than 10% of disclosed funding, though emerging ecosystems in Japan and Australia show potential for growth.

Which companies have patented the most impactful technologies in the microbiome space recently?

Over 8,000 dysbiosis-related patents were filed between 2005-2024, with the United States leading at 53.9% of filings and Europe contributing 24.2%.

AOBiome filed nine patents in Q3 2024, the highest quarterly total, followed by Fonterra with five patents, and both Seed Health and Novonesis with four patents each. The main International Patent Classification codes focus on bacterial-based therapeutics (44.8% of patents), diagnostics (15.9%), and prebiotic formulations.

Seres Therapeutics holds composition and use claims for consortia defined by 16S rDNA analysis in both US and European jurisdictions. Vedanta Biosciences patents proprietary consortia and manufacturing methods, particularly for their CARB-X-funded VE707 program. MaaT Pharma maintains orphan drug and manufacturing patents for microbiota ecological therapeutics.

The patent landscape shows increasing sophistication, with recent filings focusing on strain-specific compositions, manufacturing processes, and biomarker applications rather than broad microbiome concepts. This evolution reflects industry maturation and the need for defensible intellectual property positions as companies approach commercialization.

If you want actionable data about this market, you can download our latest market pitch deck here

How much total investment was made in the microbiome industry globally in 2024 and 2025?

Disclosed funding reached approximately $750 million in 2024 for therapeutics and consumer applications, with Indigo Agriculture's $1.2 billion agricultural round bringing the total above $1.95 billion.

Through mid-July 2025, approximately $800 million in additional funding has been disclosed, including continued support for Indigo Agriculture. The cumulative disclosed total for 2024-2025 exceeds $1.55 billion, though industry experts estimate the real total surpasses $2 billion when including undisclosed deals and smaller funding rounds.

Live biotherapeutic products capture the majority of therapeutic funding, with single-strain and defined consortia approaches receiving preferential investor attention. Agricultural applications represent the largest single category due to Indigo Agriculture's massive funding round, though human health applications show more diverse investment activity.

Expected 2026 trends include Series B and C expansion rounds following Phase 2 clinical readouts, increased ARPA-H and Horizon Europe funding commitments, and heightened corporate venture capital activity. Regulatory clarity for live biotherapeutic products should drive larger funding rounds as companies approach commercialization milestones.

What trends are shaping investor and corporate interest heading into 2026?

Clinical validation through Phase 1 and Phase 2 data represents the primary driver of investor interest, with platform versatility and strategic co-development pathways increasingly important for larger funding rounds.

Regulatory milestone alignment becomes critical as investors seek companies with clear paths to FDA approval following Seres Therapeutics' VOWST™ success. Proximity to pharmaceutical hubs influences investment decisions, with Boston and San Francisco Bay Area companies receiving disproportionate attention from venture capital firms.

Corporate venture capital participation increases significantly, with pharmaceutical companies using strategic investments to access microbiome platforms. Government funding through ARPA-H and European Innovation Council grants validates technical approaches and reduces early-stage risk for private investors.

The shift toward precision medicine applications drives interest in companies developing patient-specific microbiome interventions rather than one-size-fits-all approaches. Platform technologies that enable multiple therapeutic applications receive higher valuations than single-indication programs, reflecting investor preference for scalable business models.

Planning your next move in this new space? Start with a clean visual breakdown of market size, models, and momentum.

Which early-stage microbiome startups show the fastest growth and could become leaders by 2026?

Kanvas Biosciences demonstrates rapid traction with their spatial microbiome mapping platform, securing $12.5 million Series A funding from strategic investors including Merck Ventures for drug discovery applications.

Holobiome shows strong momentum in gut-brain axis applications with $9 million seed funding from Unilever Ventures and J&J Innovation, indicating commercial validation of their approach. Freya Biosciences' $10.4 million Gates Foundation grant for vaginal microbiome immunotherapies positions them in an underserved therapeutic area with significant market potential.

Ancilia Biosciences advances CRISPR-based bacterial vehicle therapies with ARPA-H funding, representing next-generation engineered approaches. Siolta Therapeutics' $12 million Gates Foundation support for inflammation live biotherapeutics targets broad inflammatory conditions beyond traditional gastrointestinal applications.

Z-Biotics demonstrates consumer market traction with synthetic probiotics, indicating potential for direct-to-consumer business models. These companies combine novel technical approaches with strategic investor validation, strong intellectual property positions, and clear paths to clinical or commercial milestones within 12-18 months.

Conclusion

Sources

1. Quick Market Pitch - Microbiome Funding
2. Vedanta Biosciences Press Release
3. IP Group Portfolio News
4. Microbiotica Genentech Collaboration
5. Securities.io Microbiome Companies
6. Biose News
7. Global Venturing Corporate Investors
8. Biocodex Microbiota Foundation Grant
9. Weston Foundation Microbiome Funding
10. Danone Fellowship Awards
11. Nature Yakult Global Grants
12. University of Chicago Microbiome Startups
13. Biosafe Probiota Insights
14. Microbiome Times Danone Acquisition
15. Seres Therapeutics Financial Results
16. Gut Microbiota for Health
17. NCBI Patent Analysis
18. Pharmaceutical Technology Patent Activity
19. Hoiberg Microbiome Report
20. F6S Microbiomics
21. Research and Markets Report
22. Business Research Company
23. Seedtable Best Microbiome Startups