Microbiome patents have surged over the past two decades, mirroring a profound transformation in biomedical science. Once an obscure scientific niche, the microbiome has emerged as crucial to understanding health and disease, with considerable implications for nutrition, therapeutics, diagnostics, and personalized medicine. This has been accompanied by a parallel surge in patenting activity, particularly in the United States, as researchers, startups, and pharmaceutical companies race to secure intellectual property rights in this rapidly evolving field.
This article explores the key developments shaping the microbiome patenting arena. Our focus will be on US patents and applications, particularly those from the last 15 years, with a closer look at filings since January 2023 to capture the most recent trends. To encompass the field’s full diversity and depth, we apply broad inclusion criteria, focusing on patents and applications that mention “microbiome,” “microbiota,” “microflora,” or their related variants in the title, abstract, or claims.
The origins of the microbiome patent boom
The microbiome patent boom traces back to the mid-2000s, when advances in high-throughput DNA sequencing allowed researchers to characterize complex microbial communities without relying on traditional culture techniques. The arrival of metagenomics enabled scientists to map entire ecosystems in the human body, and the initial wave of microbiome-related patent filings coincided with the early years of the funded Human Microbiome Project initiated by the National Institutes of Health (NIH). By 2015, the filings began to accelerate sharply, peaking around 2021, with nearly 100 US patents granted each year referencing microbiome-related terms.
Signs of a maturing patent landscape
Recent data suggest this growth may be stabilizing (see Figure 1). This apparent plateau could reflect a maturing and increasingly crowded field, one increasingly marked by overlapping claims, examiner scrutiny, and the limits of what is patentable. Early filings frequently pursued very broad claims, sometimes encompassing entire microbial classes, and were often founded on high-level observational discoveries. These initial applications were also drafted before the full impact of the Supreme Court’s decisions affecting subject-matter eligibility under 35 USC §101. With litigation in the field still rare and only beginning to take shape, these strategies remain largely untested in court, leaving uncertainty about what will ultimately withstand judicial scrutiny.
Two notable exceptions include a decision in the post-grant review challenge of the University of Chicago’s US Patent No. 9,855,302, and the jury decision in Ferring v. Finch involving several FMT-related patents owned by Finch Therapeutics Group Inc. Each of these challenges ultimately supported the microbiome side of the claimed inventions, but, given “n” of 2 for the dataset, it remains to be seen whether claims of other patents with similarly broad language will withstand challenge. An evolving matter to monitor is University of Tokyo & Vedanta Biosciences v. Seres Therapeutics, Inc., Aimmune Therapeutics, SPN, the Nestlé entities, and NHS Rx License GmbH, a federal action pending in the US District Court for the District of Delaware.
Expanding beyond the gut
Scientific and patenting focus is diversifying beyond the gastrointestinal tract. Dense microbial communities are being studied in the skin, lungs, reproductive tract, and other sites, each with its own emerging therapeutic and diagnostic implications. Similarly, microbial players beyond bacteria, particularly bacteriophages, are gaining attention, and patenting activity is beginning to reflect this shift.
Key trends shaping microbiome IP
As the microbiome patent landscape matures, innovators and practitioners should watch these emerging trends:
- Refined claim strategies — Microbiome patent claims are shifting toward narrower, more precise drafting, as applicants and the US Patent and Trademark Office (USPTO) alike become more discerning in framing microbiome-related inventions. Filings increasingly target consumer-oriented products as opposed to a strictly pharma-oriented approach.
- Microbial definition challenges — Applicants are moving away from simple taxonomic definitions and toward functional specificity or genomic characterizations of microorganisms, reflecting both scientific complexity and legal pragmatism.
- Rise of microbial consortia — Many filings now emphasize microbial communities, often coupled with compositional ratios of constituent microbes, rather than single strains, acknowledging the ecological complexity and therapeutic potential of multi-species formulations.
- Diagnostics on the rise, despite legal uncertainty — Microbiome diagnostic applications involving microbiome data are increasing, even as 35 USC §101 eligibility challenges persist. The predictive power of complex microbiome profiles and their potential in personalized medicine appear to outweigh the patent eligibility risks for a number of innovators.
- Expanding therapeutic targets — Microbiome therapeutics are expanding beyond gut-related disorders to encompass an expanding list, including dermatology, oncology, neurodegenerative diseases, metabolic disorders, and more.
- Postbiotics and beyond — There is growing interest in claims focused on non-living microbial products, such as postbiotics, along with formulations involving prebiotics, probiotics, and synbiotics. These offer potentially more straightforward paths to regulatory and patent approval.
- AI-microbiome convergence — An exciting frontier lies at the intersection of microbiome science and artificial intelligence. AI’s ability to process high-dimensional, complex datasets could unlock powerful predictive and therapeutic tools for microbiome research. The USPTO has also recently issued guidance on inventorship, eligibility declarations, and updated MPEP guidance signaling its openness to patenting AI inventions, which could further accelerate this convergence.
- Beyond human health — While human therapeutics dominate, microbiome innovations and patent filings are beginning to spill into adjacent sectors, such as agriculture, animal health, environmental science, and food technology.
Landmark microbiome IP litigation to watch
With litigation in the microbiome space still rare, a handful of early decisions are beginning to offer guidance on how these patents will fare under judicial scrutiny.
In Post-Grant Review No. PGR2019-00002, the Patent Trial and Appeal Board invalidated all claims of U.S. Patent No. 9,855,302, owned by the University of Chicago and licensed to Evelo Biosciences. The patent claimed methods of treating cancer using an immune checkpoint inhibitor combined with Bifidobacterium. The board found the claims lacked enablement due to the breadth of checkpoint inhibitors recited, and the specification’s limited supporting data for specific combinations. Notably, it did not find the genus-level microbial definition inherently problematic, since the specification was found to adequately guide a skilled artisan to relevant taxa, crediting the multi‑species examples and accompanying description.
The claims also failed on obviousness grounds, with the board finding sufficient motivation to combine prior art references describing (i) an anti‑PD‑L1 antibody treatment, and (ii) Bifidobacterium longum inhibition for the same cancer type (colon cancer). A key lesson: Functional claim language may offer stronger footing against obviousness challenges than purely compositional claims. For further analysis, see our prior coverage of enablement, obviousness, and broader implications for microbiome therapeutics.
In Ferring Pharmaceuticals Inc. v. Finch Therapeutics Group, Inc., a Delaware jury upheld the validity of Finch’s fecal microbiota transplant patents and found Ferring’s REBYOTA® product to be infringing. Ferring had argued that the asserted product and system claims were obvious and that the method claim lacked adequate written description support, but the jury disagreed. The decision signals that well-drafted microbiome claims — particularly those tied to specific formulations and delivery systems — can withstand validity challenges at trial. Ferring may appeal.
A third case worth monitoring is University of Tokyo & Vedanta Biosciences v. Seres Therapeutics, Inc., filed in August 2024 in the District of Delaware. The suit alleges that Seres’ FDA-approved product Vowst® infringes several patents directed to defined Clostridium-based approaches. Unlike the broader fecal transplant claims at issue in Ferring, these patents cover more precisely characterized microbial formulations: a “purified bacterial mixture of at least two live bacterial strains belonging to Clostridium clusters IV and/or XIVa” (US 9,433,652), “spore-forming fraction of human fecal matter” (US 9,662,381), or “one or more purified live bacterial strains belonging to Clostridium clusters IV or XIVa” (US 10,555,978; US 11,090,343). A decision on the merits could establish important precedent on claim scope and infringement standards for next-generation microbiome therapeutics. The case remains ongoing.
From shifting claim strategies to early courtroom battles, these developments merit close attention as patent trends, legal challenges, and strategic considerations continue to shape the next phase of microbiome innovation. Whether you are a patent professional, microbiome researcher, investor, or policymaker, this remains a compelling and dynamic intellectual property frontier to watch.
