Abstract
Active management of the microbiome of agriculturally important plants promises to optimize the reliability, resource use, and environmental impact of food production by enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance. 1 To make this promise a reality, further investments need to be made to better understand, and reliably manage, plant-microbiome interactions in the context of modern agricultural systems. It is a simple commercial reality that these investments will not be made without a realistic expectation of a financial reward, which depends in part on the availability of strong protection for any new intellectual property generated. Given the significant changes in many aspects of U.S. patent laws over the last several years, there is a need to assess and adapt patent portfolios currently protecting or being built around new technologies for managing the plant microbiome.
Patent Subject Matter Eligibility
To be entitled to a patent, a claimed invention must satisfy certain patentability requirements. Perhaps the most basic requirement is that the subject matter sought to be patented is in fact eligible for patent protection. The eligibility requirement is established by 35 U.S.C. § 101: “[w]hoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor. … ” This broad statutory eligibility has been limited by the judicially recognized exceptions that “phenomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972).
The area of subject matter eligibility under 35 U.S.C. § 101 is of special relevance to microbiome-related technologies because inventions in this field often involve the use of naturally occurring microorganisms, and/or the application of the laws of nature governing the interaction between the microbiome and the host plant, i.e., phenomena of nature. Therefore, care must be exercised when trying to patent microbiome-related inventions to ensure that the claims are directed to patent eligible subject matter rather than non-eligible phenomena of nature.
The Supreme Court's Eligibility Analysis
Patent eligibility under § 101 is analyzed using a two-step process laid out by the Supreme Court in Mayo v. Prometheus, 566 U.S. 66 (2012) and clarified in Alice v. CLS Bank, 573 U.S. (2014). The first step asks whether a claim is directed to a judicially recognized exception, i.e., natural product, natural phenomenon, or abstract idea. If the answer is no, then the claimed subject matter is patent eligible. If the answer is yes, however, the claim is further examined. Step two asks whether the additional elements recited in the claim, considered both individually and as an ordered combination, “transform the nature of the claim” into a patent eligible application by reciting an “inventive concept” that is “sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.” Mayo at 72-73. For step two of the analysis, the judicially recognized exception is treated as if it was already part of the state of the art. In Mayo, the Court found the method claims ineligible for patenting because, in addition to a natural phenomenon, they only recited elements that were “well known in the art” and represented “well-understood, routine, conventional activity previously engaged in by scientists in the field.” Id. at 79-80.
In view of the Supreme Court's arguably ambiguous “significantly more” test, the case law related to patent eligibility for biotech inventions remains inconsistent and unsettled. Unfortunately, this has created uncertainty among inventors and investors alike.
USPTO Guidance
The United States Patent and Trademark Office (USPTO) examines the eligibility of claims directed to nature-based products, including microorganisms or compositions comprising a microorganism, according to the above outlined two-step process. To facilitate examination of patent applications, the USPTO created Eligibility Examples representing a variety of nature-based compositions, including bacterial mixtures and a genetically modified bacterium, and methods of using thereof. 2 Each Example provides a fact pattern, a list of claims, and an eligibility analysis for each claim. The Examples provide a useful guide for what type of subject matter is considered patent eligible by the USPTO in view of current case law.
In the first step, the examiner determines whether the claim is directed to a product of nature. Products of nature include both naturally occurring products and man-made products that are not “markedly different” from naturally occurring counterparts. Thus, the examiner must determine if there is any marked difference between a claimed product and its naturally occurring counterpart. The Eligibility Examples indicate that a “marked difference” for the purpose of eligibility can include structural differences (e.g., difference in molecular structure, crystal forms, amino acid sequence, or genetic composition) as well as functional ones (e.g., composition with increased stability, increased solubility, or new activity). If the claim is directed to a product of nature, the examiner determines in the second step whether the claim includes an element or combination of elements in addition to the product of nature so that the claim, when viewed as a whole, amounts to significantly more than the product of nature. Therefore, drafting composition claims so that they are not considered to be “directed to a judicially recognized exception” under step one offers the safest path to patent eligibility as it altogether avoids the step two analysis. One way to achieve this goal is to ensure that the claimed compositions are “markedly different” from their naturally occurring counterpart.
Isolated and Genetically Modified Bacterium Example
Claims to an isolated naturally occurring microorganism are not considered patent eligible because they are unchanged from their natural state and do not have markedly different characteristics. However, as confirmed by the Supreme Court in its landmark 1980 Diamond v. Chakrabarty decision, claims directed to a genetically modified microorganism are patent eligible because changes in biological function between a claimed product and its natural counterpart can demonstrate markedly different characteristics.
This concept is demonstrated in the USPTO's “Genetically Modified Bacterium” patent eligibility example. The example discusses the eligibility of a sample claim directed to “a bacterium from the genus Pseudomonas containing therein at least two stable energy-generating plasmids, each of said plasmids providing a separate hydrocarbon degradative pathway.” The example provides that while there are naturally occurring Pseudomonas bacteria with one stable energy-generating plasmid, no naturally occurring Pseudomonas bacteria is known to have more than one stable energy-generating plasmid. Under this fact pattern the sample claim is considered patent eligible because the claimed bacterium is markedly different from its natural counterpart both functionally and structurally. Functionally, the claimed bacterium is markedly different from its natural counterpart because it is capable of degrading two different hydrocarbons whereas the naturally occurring counterpart can degrade only one. Structurally, the claimed bacterium is markedly different from the natural counterpart because it has been modified to include more than one plasmid. Thus, a recombinant microorganism and its naturally occurring counterpart can have markedly different structural characteristics based on the mere presence of a transgene or if the transgene confers a new activity on the host cell.
Bacterial Mixtures Example
According to the USPTO's “Bacterial Mixtures” eligibility example, a claim to a composition comprising a mixture of naturally occurring bacteria can be patent eligible if the mixture is “markedly different” from its naturally occurring components. The example starts with the fact pattern of Funk Brothers, a case in which the Supreme Court found a claim to a mixture of bacteria not eligible for patenting, and finishes with a hypothetical fact pattern under which the USPTO would consider a claim to a bacterial mixture patent eligible. Funk Bros. Seed Co. v. Kalo Co., 333 U.S. 127 (1948).
The claim considered in Funk Brothers was directed to “an inoculant for leguminous plants comprising a plurality of selected mutually non-inhibitive strains of different species of bacteria of the genus Rhizobium, said strains being unaffected by each other in respect to their ability to fix nitrogen in the leguminous plant for which they are specific.” The Supreme Court found the claim ineligible for patenting because there was no indication in the patent that the claimed mixture was different, structurally, functionally, or otherwise, from bacteria that occurs in nature. In the absence of any indication of a marked difference, the claim was understood to be directed to the naturally occurring bacteria. The USPTO's hypothetical fact pattern states that a mixture of Rhizobium californiana and Rhizobium phaseoli can infect a host plant that neither bacterium would infect alone. Under this fact pattern, the USPTO would consider a claim to “an inoculant for leguminous plants comprising a mixture of Rhizobium californiana and Rhizobium phaseoli” patent eligible, provided that the claimed combination of bacteria does not occur in nature. Thus, the functional difference of infecting a new host would be considered a marked difference that confers patent eligibility on the hypothetical claim.
Patenting the Plant Microbiome
Microbiome management involves the selection, cultivation and application of beneficial microorganisms. A patent portfolio protecting a microbiome management system can include composition claims directed to the microorganisms and seed-microorganism combinations, method claims directed to the large scale production of the microorganisms, and method claims directed to the selection and application of optimal microorganisms. All of these claims will recite a nature-based product and/or a natural phenomenon and consequently will be examined for subject matter eligibility at the USPTO.
Microorganism-Coated Seeds
Coating seeds with an isolated microorganism provides a mechanism for manipulating the plant microbiome. To be patent eligible, the microorganism coated seed has to be markedly different from a seed found in nature, which is generally associated with microorganisms. Additionally, the claim has to be drawn narrowly enough to not encompass a seed found in nature. The coated seed and its natural counterpart may be markedly different if the seed or the microorganism has been modified to change their properties (e.g., their genetic make-up or shelf-life). Alternatively, the coated seed may be markedly different if the particular seed-microorganism combination does not occur in nature. In cases where a marked difference cannot be established, method/process claims using that coated seed in a non-natural way can offer a path to patent eligibility.
Method of Culturing Microorganisms
The availability of methods for efficiently producing microorganisms on a large scale is a precondition for the active management of the microbiome of agriculturally important plants. Given that many components of the microbiome are not amenable to large-scale production using current technologies, the development of new culture methods is a way for companies to gain a competitive advantage. A recent Court of Appeals for the Federal Circuit decision found that claims directed to a “method of producing a desired preparation of multi-cryopreserved hepatocytes” are patent eligible, even if the process uses a product of nature and even if the transformation is governed by the laws of nature. Rapid Litigation Management v. Cellzdirect, 827 F.3d 1042 (Fed. Cir. 2016) (“This type of constructive process, carried out by an artisan to achieve ‘a new and useful end,' is precisely the type of claim that is eligible for patenting.”). Cellzdirect confirms the USPTO's position expressed in the Eligibility Examples that process claims are generally patent eligible unless they are drafted to claim a judicially recognized exception itself, such as “a method of providing an apple.” Thus, claims directed to methods of producing microorganisms are expected to be patent eligible.
“Customized” Microbiome Management
With increased understanding of the rules governing the microbiome's effect on plant growth, nutrient use efficiency, and disease resistance under particular weather and soil conditions will come the ability to provide “customized” microbiome management services that have been optimized for particular combinations of plant genotype and environmental conditions. Such “customized” services would have to include the steps of detecting the genetic and environmental conditions present at the site to be treated, determining the optimal treatment regimen, and executing the treatment. “Customized” microbiome management would be very similar to personalized medicine applications in that they both rely on diagnostic methods to deliver customer-specific treatment.
Generating the information of which microorganism(s) provides benefit to a specific plant under particular weather/soil conditions is central to the development of a customized microbiome management plan. While the correlations between plant genotype, soil/weather conditions and the microbiome themselves are not eligible for patenting, their use may be protected by well drafted method claims. Court decisions on the patent eligibility of diagnostic method claims provide a road map for how to draft patent eligible method claims. In Mayo v. Prometheus, the Supreme Court found patent ineligible claims broadly drawn to capture all uses of a diagnostic correlation, regardless of the reagents employed or the starting samples used. Mayo at 77-80. In the Court's analysis, once the newly discovered diagnostic correlation is treated as if it were part of the state of the art, the remaining elements merely recite routine, conventional, and well-understood steps that cannot provide the inventive concept needed to transform the methods into patent eligible subject matter. Therefore, to be considered eligible, a diagnostic method claim may need to recite the use of an assay or reagent that was not well known and in common use. Alternatively, if all elements of the claim were well known and in common use, it may need to recite a new, inventive combination of these elements.
Combining the step of detecting the genetic and environmental conditions present at the site to be treated with the step of treating the site into a single method claim may provide an alternative path to patent eligibility. While there is no post-Mayo appellate decision confirming the eligibility of claims combining diagnostic and treatment steps, they are generally considered patent eligible. See Classen Immunotherapies, Inc. v. Biogen Idec, 659 F.3d 1057 (Fed. Cir. 2011); Bristol Myers Squibb Co. v. Merck & Co., No. 14-1131 (D. Del. Mar. 17, 2016); Bristol Myers Squibb Co. v. Merck & Co., No. 15-572 (D. Del. Mar. 29, 2016).
Conclusion
Although isolated bacteria and mixtures of isolated naturally occurring bacteria are not patent eligible, many aspects of managing the plant microbiome may very well be. For example, recombinantly modified microorganisms, mixtures of microorganisms and seed-microorganism combinations that do not co-exist in nature and possess a new activity are likely considered patent eligible. Methods for large scale production of microorganisms and methods for the selection of optimal microorganisms may also be protected by patents. Given the significant changes in U.S. patent law governing subject matter eligibility over the last several years, keeping a close eye on this developing field is critical to the development and maintenance of a strong patent portfolio around new technologies for managing the plant microbiome.