The Emergent Microbiome: A Revolution for the Life Sciences Part XI: Agriculture and the Microbiome
Knowledge of, and interest in, the human microbiome has rapidly expanded in recent years: each week, there seems to be additional advancements in our understanding of the microbial communities that call our bodies home. As investigations into these microbial communities and their impact on our health continue to develop, many researchers have rightfully begun to untangle the web of microbial communities external to us (See Part VII, The Microbiology of the Built Environment). In particular, we have observed an increased interest in the microbial communities associated with agriculture and crops. Having a clearer understanding of agriculture-associated microbial communities, and how they can be manipulated and modulated, will play an increasingly important role in the safety and security of our food supply. In fact, we have seen several encouraging efforts devoted to the advancement of microbiome research in agriculture, and we expect to see a subsequent increase in the need for intellectual property protection in this space. Importantly, we also see a clear path forward for patent-eligible inventions in this historically challenging area. While this article will focus on agriculture and the microbiome, we have also observed an increase in the attention being given to livestock production and the microbiome. In an upcoming installment of The Emergent Microbiome, we will address the history, importance, and advancements with respect to this field of research and related intellectual property issues and challenges.
A Brief History
Although there have historically been challenges with the patenting of bacterial communities or inoculants for plants, we do, in fact, see a clear path forward for the patent eligibility of advancements in this space. The governing precedent has been Funk Brothers Seed Co. v. Kalo Inoculant Co., a 1948 Supreme Court case ruling that held that the use of naturally occurring bacterial strains, or combinations thereof, in supplementing the growth of crops was no more than the attempt to patent a naturally occurring product. As a result, the inoculants were deemed to be patent ineligible. Interestingly, however, there were several patent applications filed between the 1970s and late 1990s that focused on the use of microorganisms and seeds, including methods to coat seeds with various materials such as microbial communities (Appendix A). These patents represented an advancement over Funk Brothers. Some of the claims are directed to methods of coating seeds or associating microbial components with the seeds and not merely attempting to patent a combination of naturally occurring microbes that can supplement plant growth.
Moreover, in recent years, we have seen a further development of patents and patent applications directed to the association of microbial communities with agricultural crops (Appendix B). In particular, many researchers have emphasized methods of creating associations of plants and microbial communities beyond what had been proposed in these patents from the 1970s-1990s. For example, some applications have focused on the association of microbial communities with the inside of the seed rather than merely an outer coating.
Additionally, in the December 2014 subject matter eligibility guidance update (Nature-based product examples- Example 6), the USPTO provided an example directed to the patent eligibility of bacterial mixtures in association with plants. The first claim example was modeled after the Funk Brothers case and is not patent eligible as written. The second claim focuses on an inoculant that harbors additive qualities that are not naturally prescribed to the individual components. These claims are exemplified as patent eligible because they provide “something more” than what is found in nature.
Taken together, we believe that this progression of pioneering patents from the 1970s-1990s followed by more recent developments suggests a promising landscape for the patent-eligibility of advancements made in this space.
The importance of plant microbiomes and subsequent business related developments
According to the most recent USDA Census of Agriculture (2012), the market value of all crops sold in 2012 was just over 200 billion dollars, yet questions remain about the sustainability of production methods in light of an ever-increasing demand and growing global population. There have been many efforts, both public and private, into finding ways of increasing the sustainability, productivity, and security of crop production by better understanding the interaction between microbial communities and plant growth.
In 2016, the National Microbiome Initiative (NMI) was established with the aim of “foster[ing] the integrated study of microbiomes across different ecosystems,” including those of plants and livestock. In fact, more than 120 million dollars were dedicated to the NMI, including approximately 16 million from the USDA to better understand microbial communities associated with crops, livestock animals, and fish in addition to the communities found in the air, water, and soil, as they are implicated in the growth, maintenance, and production of agricultural and animal products.
Although the NMI has served as an important call to increase research efforts in the area of plant and crop microbiome research, perhaps the most interesting advances have been made in the private sector and are related to ‘microbials’ for improving crop growth, yield, and tolerance. Although established companies such as Dupont, Monsanto, and Bayer have entered the microbials space, smaller start up companies have made especially interesting and important contributions. In particular, Indigo Agriculture, New Leaf Symbiotics, and BioConsortia have each contributed important advances. Indigo, formerly known as Symbiota, has developed technology using bacteria to enhance the growth of crops under conditions of stress, such as limited access to water. Indigo has focused primarily on the bacteria found inside the growing plant (endophytes) rather than those found on it or around it in the soil. Association of plants with particular bacterial strains, it is thought, will help these plants to better withstand conditions of stress that can affect crop production and yield. Indigo announced its first commercial product, Indigo Cotton, in the summer of 2016 and reported at the beginning of 2017 that test plantings in areas of Texas resulted in significant increases in crop yield per acre. In addition to Indigo Cotton, the company has also developed Indigo Wheat.
Similarly, NewLeaf Symbiotics is pioneering technology using a family of bacteria that is typically associated with plants called pink-pigmented facultative methylotrophs (PPFMs). Association of PPFMs with certain plants has been shown to result in faster growing plants that produce higher crop yields. BioConsortia has also devoted its efforts to understanding how microbial populations can increase crop health and yield and developed a proprietary approach called Advanced Microbial Selection (AMS), whereby plants that have been exposed to various bacterial communities are selected for changes that result in growth improvements. These beneficial communities are then further analyzed for future use in wide-ranging agricultural applications. BioConsortia has focused on crops ranging from wheat to tomatoes to turf.
In light of these recent efforts and advancements and the burgeoning promise of understanding plant microbiomes, researchers have called for the standardization of priorities to better streamline research efforts and findings. In March 2017, Bubsy, et al. called for five research priorities concerning plant microbiomes and agriculture. In particular, the authors called for both the development of better model systems for plants and for defining core microbiomes in these model systems to better understand how microbial communities can be manipulated and modulated for agricultural applications. Although companies like Indigo have made considerable advancements in this space, it is possible that standardizing research efforts and building a strong foundation to back up these efforts could lead to even more successful attempts at modulating crop growth and yield in the future.
As research into the plant microbiome is standardized and as companies continue to develop novel technologies related to plant microbiomes, we expect there to be an increase in the need for associated intellectual property protection. We believe that the push for even higher quality and more standardized research, alongside the historical progression of patents in this area, will provide a fruitful and productive space for innovation and subsequent legal protections.
Appendix A: Patents and patent applications related to seed coating methods and association of microbial communities with seeds
|Application/ Patent Number||Inventor||Assignee||Title||Filing Date
|US5916029A||Smith and Osburn||LiphaTech, Inc.||Process for producing seeds coated with a microbial composition||June 26, 1996|
|US5113619A||Leps and Thompson||Leps and Thompson||Method of adhering bacteria to seed and composition therefor||October 5, 1990|
|US4879839A||Gago and Detroz||Solvay & Cie.||Coated seeds and process for preparing them||April 4, 1988|
|US4367609A||Lloyd||Coated Seed Ltd.||Use of microorganisms in conjunction with seeds||July 14, 1981|
|US4149869A||Lloyd||Coated Seed Ltd.||Seed coating techniques||August 30, 1977|
Appendix B: Recent patents and patent applications related to agriculture and the microbiome
|Application/ Patent Number||Inventor||Assignee||Title||Filing Date
|WO2016201284 A3||Rioux||Newleaf Symbiotics, Inc.||Antifungal methylobacterium compositions and methods of use||10-Jun-16|
|US 20160235074 A1||von Maltzahn, et al.||Indigo Ag, Inc.||Methods of Use of Seed-Origin Endophyite Populations||3-May-16|
|US20160316760 A1||Ambrose, et al.||Indigo Agriculture, Inc.||Isolated Complex Endophyte Compositions and Methods for Improved Plant Traits||29-Apr-16|
|WO 2016069564 A1||Jones and Bogosian||Newleaf Symbiotics, Inc.||Methods and compositions for controlling corn rootworm||27-Oct-15|
|US 9408394 B2||Von Maltzahn, et al.||Indigo Agriculture, Inc.||Endophytes, associated compositions, and methods of use thereof||26-Jun-15|
|EP 3145293 A1||Meadows-Smith, Wigley, and Turner||Bioconsortia, Inc.||Integrated plant breeding methods for complementary pairings of plants and microbial consortia||22-May-15|
|US 20140283441 A1||Holland, BiBello, and Carlton||Newleaf Symbiotics, Inc.||Method for Increasing Algae Growth and the Use Thereof in Production of Algae-Derived Biofuels and Other Chemicals||11-Jun-14|
|US9181541 B2||Bogosian||Newleaf Symbiotics, Inc.||Microbial fermentation methods and compositions||31-May-13|
– Nicholas Vincent and Anthony D. Sabatelli, PhD, JD
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