We have been working in and following developments regarding microbiome IP for over 10 years, and what has unfolded in that time is remarkable. As the technology has matured and the prior art has grown more crowded, the field has transformed regarding both claim scope and claim structures.
To identify and evaluate current trends in claim types and subject matter descriptions, we searched for patents that mention “microbiome,” “microbiota,” “microflora,” or related variants in the title, abstract, or claims. Of the 154 U.S. patents granted in 2025 that our search identified, we manually selected 82 with claims directly related to the microbiome; for example, describing microbes, compounds intended to influence or modulate the microbiome, or the use of microbiome-related data for an application. We focused primarily on the independent claims, while also considering dependent claims where they reveal additional strategic nuances. The picture that emerges is compelling.
Market expansion meets claim discipline in microbiome innovation
Two concurrent developments stand out. The first is a striking orientation toward consumer-facing products: a notable proportion of the patents in this set (38 of 82; 46%) include claims directed to consumer-oriented products, such as dietary supplements, cosmetic formulations, oral care products, digital health devices, and pet health compositions. These are often framed around general wellness outcomes, maintenance of physiology, or risk reduction rather than the disease-specific or defined therapeutic endpoints that have characterized conventional pharmaceutical microbiome claims. This consumer orientation likely reflects recognition that consumer channels offer broader markets and faster paths to commercialization, alongside increased crowding and regulatory complexity in patenting in traditional pharma. We will examine this trend and its implications in detail in the next chapter of this series. The second development is a move toward tighter, more precisely defined claims, reflecting growing sophistication on the part of both applicants and the USPTO in how microbiome inventions are framed and examined. This trend, the focus of the remainder of this chapter, may also prove predictive of how enforcement and validity challenges unfold as the microbiome space matures.
Independent Claim Types—Overview and Distribution
One aspect that immediately becomes apparent is that method claims dominate the dataset. 67 of the 82 patents include at least one independent method claim (81.7%), and 59 of those (72%) are method-only. Patents with more than one independent claim type often pair method claims with systems, machines, or computer-readable media in data, diagnostic, and AI contexts. Even accounting for U.S. restriction practice, where it is common for the USPTO to separate compositions and methods into distinct groups and restrict examination to one at a time, the signal is clear: method claims have become the primary vehicle for securing microbiome-related claim protection as composition claims face higher prosecution hurdles in this space. Notably, the method claims being granted are not mere fallbacks for composition claims; they are deliberately engineered to combine measurable parameters, clinical endpoints, and subject stratification in ways that sharpen scope and strengthen defensibility.
Where composition claims are granted (15 of 82 patents; 18.3% have only non-method independent claims, of which 12 are composition-only), those claims often include references to specific deposited microbes and are reinforced by additional narrowing strategies. Many composition-only patents also extend their coverage into method space through dependent claims, preserving method-of-use protection within a composition framework. Across both claim types, the direction is consistent: claims are becoming more precisely defined and more strategically layered than earlier.
Microbial Identity Strategies—How Claims Define Their Biological Subject Matter
More than half of the patents in this dataset (47 of 82; 57%) include at least one independent claim that directly recites microbes or microbial descriptions. Within those 47, wild-type microbial descriptions predominate: single species or strain claims account for 10 patents (21.3%); defined mixed compositions or consortia of two or more species appear in 12 (25.5%); and undefined donor-derived communities, such as FMT or fecal preparations, appear in 6 (12.8%). Another 15 patents (31.9%) define microbes broadly at the genus or family level but layer additional narrowing elements. Engineered microbes, though a small cohort of 4 patents (8.5%), represent an emerging and strategically significant category.
The identity strategies themselves are diverse and increasingly sophisticated, drawing on an expanding toolkit that includes deposit anchoring, 16S rDNA sequence thresholds, function-based definitions, quantitative taxonomic architectures, and genetic engineering, often in combination.
Deposit—Anchored Identity
Deposit anchoring ties a claim to a physical specimen held at a recognized depository, a tangible biological reference that does not shift with taxonomic reclassification or database updates. The claimed product can be compared genomically and phenotypically to the deposited strain, and the deposit satisfies the enablement and written description requirements under 35 USC §112, particularly for novel isolates or strains with significant functional variation at the strain level.
Nine patents in this dataset use deposit anchoring in their independent claims (U.S. Patent Nos. 12,194,142, 12,239,674, 12,350,299, 12,370,228, 12,419,313, 12,440,521, 12,472,211, 12,478,651, and 12,491,219). Deposited microbes are frequently paired with form and state constraints (e.g., lyophilized, spray-dried, biofilm), simultaneously aligning the claim with the actual commercial product and distinguishing it from the naturally occurring microbe.
Examples of deposit-anchored claim language include:
- “administering to a subject in need thereof a pharmaceutical composition containing an isolated strain of Lactobacillus rhamnosus LRH05, wherein the isolated strain of Lactobacillus rhamnosus LRH05 is deposited at Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH under an accession number DSM 33616.” U.S. Patent No. 12,239,674.
- “composition comprising a lyophilized or spray-dried Bacillus velezensis strain BV379 or progeny thereof, wherein a sample of the strain has been deposited under ATCC Accession No. PTA-127359.” U.S. Patent No. 12,350,299.
A deposit need not mean a scope restricted to that single organism, however. At least four distinct breadth-extending mechanisms appear across these claims, employing creative mechanisms to extend coverage beyond the exact deposited strain, while retaining the precision and enforceability that deposits provide:
- U.S. Patent No. 12,350,299 claims a “composition comprising a lyophilized or spray-dried Bacillus velezensis strain BV379 or progeny thereof,” extending protection to derivatives arising from the deposited strain through natural reproduction or passaging.
- U.S. Patent No. 12,370,228's independent claim requires a composition of three specific bacterial species, but requires only “one or two bacteria of the composition” to be selected from a group of specifically deposited strains (Lactobacillus crispatus strain 223310, ATCC deposit PTA-127090; Lactobacillus jensenii strain 2054210, ATCC deposit PTA-127092; Lactobacillus gasseri strain 29313, ATCC deposit PTA-127091), preserving flexibility to incorporate additional species-level variants as the product evolves.
- U.S. Patent No. 12,419,313 uses average nucleotide identity (ANI) thresholds layered across independent claims. Claim 1 covers deposited bacteriophages (CJLB-4 through CJLB-15, ATCC Deposit Accession Nos. PTA-126839 through PTA-126846) “or variants of said bacteriophage which have an average nucleotide identity over the genome of ≥99.9% relative to said bacteriophage, said variants having lytic activity against Campylobacter species or strains.” Independent claim 10 broadens the ANI threshold to ≥95%, creating a tiered scope profile.
- U.S. Patent No. 12,440,521uses a live/extract alternative, claiming a “composition comprising an isolated Lactobacillus fermentum bacterial strain grown as biofilm, and/or comprising a bioactive extract of said biofilm,” wherein the bacterial strain is Lactobacillus fermentum Qi6, having Accession No. PTA-122195. This extends coverage from the living organism to its non-living derivatives, capturing both the probiotic product and its postbiotic applications.
The remaining five deposit-anchored patents take the opposite approach, tying their claims tightly to the deposited strain itself. The coexistence of tight and extended deposit claims within the same cohort underscores the strategic range now available in this space.
16S rDNA-Based Identity—A Declining Strategy
In contrast to the prevalence of deposit anchoring, only two of the 82 patents (U.S. Patent No. 12,214,002 and 12,397,022) rely on 16S rDNA sequence identity. 16S rDNA thresholds were once a standard tool for defining microbial scope, but the field has moved decisively toward other alternatives. 16S has limited resolution at the strain level, and percent-identity cutoffs can sweep in numerous related taxa or exclude intended targets. Where 16S does appear, as in U.S. Patent No. 12,397,022, it can be paired with additional identity layers rather than used in isolation.
Function-Based Definitions
Appeals courts have emphasized that structure, as opposed to function alone, is required to adequately satisfy the patent disclosure requirements under 35 USC §112. However, when used in conjunction with structural description, reference to assayable functional outputs, such as metabolite production, enzymatic conversion, or pathogen inhibition, can be useful to further define subject matter in patent claims. Select examples include:
- “a composition comprising two or more purified or isolated bacteria or spores thereof, the composition comprising: a first purified or isolated bacteria or spores thereof comprising Clostridium scindens; a second isolated or purified bacteria or spores thereof comprising Blautia hansenii or Barnesiella intestihominis; and a secondary bile acid selected from the group consisting of a deoxycholic acid, a lithocholic acid, and a combination thereof, wherein the two or more purified or isolated bacteria or spores thereof are in a formulation for administration to a subject, wherein at least one of the two or more purified or isolated bacteria or spores thereof is capable of converting a primary bile acid to a secondary bile acid...” U.S. Patent No. 12,414,969
- “administering to the subject an effective amount of a microbial composition comprising a butyrate-producing microbe, wherein the butyrate-producing microbe increases production of butyrate in the subject.” U.S. Patent No. 12,233,095.
These claims span a wide spectrum of precision. U.S. Patent No. 12,414,969 layers function (bile-acid conversion) onto named structural partners in a defined consortium, whereas U.S. Patent No. 12,233,095, at the other end, defines the microbe almost entirely by function, representing the broadest approach to function-based identity in this cohort. Function-based definitions are thus not a single strategy but a continuum, offering applicants calibrated control over the breadth-versus-precision tradeoff.
Broad Taxonomic Definitions with Layered Narrowing
Fifteen of the 47 microbe-direct patents (31.9%) define their microbes at the genus or family level without anchoring to deposits, 16S sequences, or specific functional outputs in the independent claims. These are not, however, broad claims in the traditional sense. In virtually every case, the taxonomic breadth is paired with other narrowing elements, such as co-therapy requirements, clinical endpoint gates, formulation constraints, delivery-site specifications, or patient selection criteria, which allow claims to maintain flexibility in microbial identity while achieving specificity through the surrounding claim architecture. We will take these up in detail in an upcoming chapter.
Engineered Microbe Identity—An Emerging Frontier
Four patents in this dataset claim engineered microbes, signaling a nascent and growing intersection between synthetic biology and microbiome innovation.
The four patents span a striking range of applications: CRISPR-modified lactic acid bacteria engineered to degrade pesticides in Monarch butterfly gut microbiomes (U.S. Patent No. 12,239,706); CRISPR/Cpf1-enhanced bacteria generating tryptophan metabolites for neurocognitive protection (U.S. Patent No. 12,318,414); CRISPR/Cas-based editing of plant-pathogenic bacteria within mixed soil communities (U.S. Patent No. 12,318,445); and recombinant gram-negative bacteria engineered to export antiviral proteins and miRNA via vesicles for treatment of herpesvirus infections (U.S. Patent No. 12,428,643). As an example, U.S. Patent No. 12,428,643 claims “a method of preventing or treating human herpesvirus infection in the gastrointestinal tract of a subject, the method comprising the oral administration of recombinant gram-negative bacteria engineered to contain a genome-integrated expression construct for expression of antiviral protein, miRNA, or both, that are exported in vesicles.”
Engineering language carries inherent strategic advantages. The non-natural transformation of the microbe strengthens patent-eligible subject matter arguments under 35 USC §101 because the claimed organism is not a product of nature. The specificity of the genetic modification, such as named constructs, identified gene targets, and defined functional outputs, supports enablement and written description requirements under §112. The engineered functionality itself additionally defines the commercial value proposition with a precision that wild-type claims rarely achieve.
Consortia as a Narrowing Strategy
Another dimension of claim refinement visible in this dataset is the use of defined multi-species consortia as a structural narrowing tool, drawing precision from compositional structure, specifying not just which organisms are present but how they relate to each other quantitatively. Of the 47 patents with independent claims directly reciting microbes, 12 (25.5%) require defined multi-species compositions. The claim frameworks that consortia employ have grown markedly more sophisticated than a simple species list, encompassing many multi-layered combinations of constraints. We will return to these frameworks in detail in a subsequent chapter.
Narrowing Strategies Beyond Microbial Identity
Across the dataset, applicants are deploying a growing set of non-identity narrowing strategies that add further layers of specificity, clinical relevance, and commercial precision to claims. These strategies fall into several broad categories: clinical and biomarker endpoints (including measurable microbial shifts, toxin DNA negativity thresholds, responder-defined microbiome profiles, and co-therapy and potentiation frameworks); delivery, site, and formulation constraints; and patient selection gates. These add clinical relevance and commercial precision to claims. We will examine these strategies, their claim architectures, and their implications in detail separately.
What emerges from this dataset is a decisive shift toward precision. The toolkit available to microbiome patent applicants is broader, more sophisticated, and more strategically differentiated than at any prior point in this field's development. Nixon Peabody’s microbiome intellectual property lawyers help innovators understand these evolving claim strategies to translate them into durable, commercially viable microbiome patent portfolios. Future analysis will examine how that toolkit is being deployed across consumer products, therapeutic targets, diagnostics, and emerging frontiers.