DCT

1:24-cv-00957

Vedanta Biosciences Inc v. Seres Therap Inc

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:24-cv-00957, D. Del., 08/20/2024
  • Venue Allegations: Venue is alleged to be proper as to Seres Therapeutics and Nestlé Health Science US Holdings, Inc. because they are Delaware corporations. Venue is alleged as to the foreign Nestlé entities on the basis that they may be sued in any judicial district where personal jurisdiction exists.
  • Core Dispute: Plaintiff alleges that Defendant’s Vowst® product, a capsule-based therapy for recurrent Clostridioides difficile infection, infringes five patents related to the use of specific bacterial compositions derived from human fecal matter to induce regulatory T cells for treating infectious and autoimmune diseases.
  • Technical Context: The lawsuit is in the field of microbiome therapeutics, a growing area of biotechnology focused on using live microorganisms to treat diseases by modulating the host's gut microbiome and immune system.
  • Key Procedural History: The complaint alleges that Defendant Seres was aware of the asserted patent family prior to launching the accused product, citing a 2017 opposition proceeding Seres filed in the European Patent Office against a related patent and Seres' public disclosures acknowledging awareness of third-party patents that could cover Vowst®. All asserted patents claim priority to a common family of applications, suggesting a closely related technical disclosure.

Case Timeline

Date Event
2010-06-04 Earliest Priority Date for all Asserted Patents
2011-06-03 U.S. National Stage Entry Date for Parent Application
2011-11-14 University of Tokyo licenses patent rights to Vedanta
2016-09-06 U.S. Patent 9,433,652 Issues
2017-04-25 Seres files opposition in European Patent Office against related patent
2017-05-30 U.S. Patent 9,662,381 Issues
2017-11-07 U.S. Patent 9,808,519 Issues
2020-02-11 U.S. Patent 10,555,978 Issues
2021-08-17 U.S. Patent 11,090,343 Issues
2021-07-01 Seres and Nestlé enter into co-commercialization agreement (approx. date)
2023-04-26 FDA approves Vowst®
2023-06-01 Defendants launch Vowst® in the U.S. (approx. date)
2024-08-20 Complaint Filed

II. Technology and Patent(s)-in-Suit Analysis

U.S. Patent No. 9,433,652 - "Composition for inducing proliferation or accumulation of regulatory T cells"

Issued September 6, 2016

The Invention Explained

  • Problem Addressed: The patent’s background section notes that while intestinal bacteria were known to influence the immune system, it was unclear "what species of bacteria constituting the intestinal commensal bacterial flora exerts the influence on the induction of regulatory T cells" (’652 Patent, col. 2:44-49).
  • The Patented Solution: The invention is based on the discovery that bacteria belonging to the genus Clostridium, when isolated from a spore-forming fraction of a fecal sample, can induce the proliferation and accumulation of regulatory T cells (Treg cells) in the colon (’652 Patent, Abstract). These induced Treg cells are described as having an immunosuppressive effect, making the bacterial compositions useful for treating diseases where immune modulation is beneficial (’652 Patent, col. 3:45-51).
  • Technical Importance: This discovery identified a specific genus of bacteria capable of modulating a key component of the immune system, providing a targeted approach for developing microbiome-based therapeutics (Compl. ¶¶ 28-29, 31).

Key Claims at a Glance

  • The complaint asserts independent claim 1 (Compl. ¶93).
  • The essential elements of claim 1 are:
    • A method of treating a human subject having an infectious, autoimmune, or allergic disease;
    • comprising administering a pharmaceutical composition with a purified bacterial mixture of at least two live bacterial strains from Clostridium clusters IV and/or XIVa;
    • wherein the strains are spore-forming bacteria; and
    • wherein the strains are isolated from a human.
  • The complaint does not explicitly reserve the right to assert dependent claims for the ’652 patent.

U.S. Patent No. 9,662,381 - "Composition for inducing proliferation or accumulation of regulatory T cells"

Issued May 30, 2017

The Invention Explained

  • Problem Addressed: The complaint describes the same technical problem as for the ’652 Patent: identifying which specific species of gut bacteria could induce regulatory T cells to maintain immune homeostasis (Compl. ¶30).
  • The Patented Solution: The invention provides a method for treating diseases by orally administering a pharmaceutical composition that comprises a "spore-forming fraction of human fecal matter" (Compl. ¶104). This composition is alleged to work by inducing the proliferation of Treg cells, thereby enhancing the patient's immune function (Compl. ¶¶ 31-32, 104).
  • Technical Importance: This technology provided a therapeutic method using a specifically prepared fraction of fecal material, rather than whole fecal matter, formulated for oral delivery to achieve a targeted immunological effect (Compl. ¶¶ 32, 44).

Key Claims at a Glance

  • The complaint asserts independent claim 1 (Compl. ¶104).
  • The essential elements of claim 1 are:
    • A method of treating a human subject having an infectious, autoimmune, or allergic disease;
    • comprising administering a pharmaceutical composition comprising a spore-forming fraction of human fecal matter;
    • wherein the composition induces proliferation and/or accumulation of regulatory T cells; and
    • wherein the composition is formulated for oral administration.
  • The complaint does not explicitly reserve the right to assert dependent claims for the ’381 patent.

U.S. Patent No. 9,808,519 - "Composition for inducing proliferation or accumulation of regulatory T cells"

Issued November 7, 2017

The Invention Explained

  • The ’519 Patent claims a pharmaceutical composition, rather than a method of treatment. The composition's active ingredient consists of a spore-forming fraction of human fecal matter, is formulated for oral administration and delivery to the intestine, and induces the proliferation of regulatory T cells (Compl. ¶117).

Key Claims at a Glance

  • Asserted Claims: The complaint identifies exemplary independent claim 17 (Compl. ¶117).
  • Accused Features: The complaint alleges that the Vowst® product itself, as a pharmaceutical capsule containing a spore-forming fraction of human fecal matter, infringes the claims of the ’519 Patent (Compl. ¶¶ 115, 119).

U.S. Patent No. 10,555,978 - "Composition for inducing proliferation or accumulation of regulatory T cells"

Issued February 11, 2020

The Invention Explained

  • The ’978 Patent claims both a pharmaceutical composition and a method of its use. The composition comprises one or more purified live bacterial strains from Clostridium clusters IV or XIVa that are isolated from a human, induce Treg cell accumulation, and are formulated for delivery to the intestine (Compl. ¶¶ 132-133).

Key Claims at a Glance

  • Asserted Claims: The complaint identifies exemplary independent claims 1 (composition) and 16 (method) (Compl. ¶¶ 132-133).
  • Accused Features: The complaint alleges that the Vowst® product itself infringes the composition claims, and that the administration of Vowst® to treat C. difficile infection infringes the method claims (Compl. ¶¶ 130-131, 135).

U.S. Patent No. 11,090,343 - "Composition for inducing proliferation or accumulation of regulatory T cells"

Issued August 17, 2021

The Invention Explained

  • The ’343 Patent claims a pharmaceutical composition and its method of use, similar to the ’978 Patent. The composition comprises one or more purified live bacterial strains from Clostridium clusters IV or XIVa that are specifically identified as "human commensal bacteria," induce Treg cell accumulation, and are formulated for delivery to the intestine (Compl. ¶¶ 149-150).

Key Claims at a Glance

  • Asserted Claims: The complaint identifies exemplary independent claims 1 (composition) and 16 (method) (Compl. ¶¶ 149-150).
  • Accused Features: The complaint alleges that the Vowst® product infringes the composition claims and that its administration infringes the method claims (Compl. ¶¶ 147-148, 152).

III. The Accused Instrumentality

Product Identification

  • Vowst® (fecal microbiota spores, live-brpk), a capsule-based pharmaceutical product, and its active pharmaceutical ingredient ("API") (Compl. ¶1).

Functionality and Market Context

  • Vowst® is an orally administered capsule containing a "bacterial spore suspension" manufactured from human fecal matter sourced from qualified donors (Compl. ¶¶ 67, 70). The manufacturing process involves treating the fecal matter with ethanol to kill non-spore organisms, followed by filtration (Compl. ¶70; Ex. G, §11). The complaint includes an image from the Vowst® Prescribing Information detailing dosage and oral administration instructions (Compl. ¶67).
  • The product is indicated for the prevention of recurrent Clostridioides difficile infection in adults (Compl. ¶66). Its purported mechanism is to "add back good bacteria to your gut" to restore the microbiome's balance and prevent C. diff from recurring (Compl. ¶68). An infographic from the Vowst® website illustrates this process (Compl. ¶68; Ex. H).
  • The complaint alleges that Vowst® contains live, spore-forming, human commensal bacterial strains belonging to the phylum Firmicutes, and specifically includes bacteria from the genus Clostridium within clusters IV and/or XIVa (Compl. ¶¶ 71-73). A table from a New England Journal of Medicine article supplement is provided as evidence for the taxonomic composition of Vowst® (Compl. ¶73; Ex. I).
  • Vowst® was approved by the FDA on April 26, 2023, and commercially launched in June 2023 (Compl. ¶¶ 77-78). Seres manufactures the product and co-commercializes it in the United States with Nestlé through a license agreement (Compl. ¶¶ 80-81).

IV. Analysis of Infringement Allegations

U.S. Patent 9,433,652 Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
A method of treating a human subject having an infectious disease... Vowst® is marketed and prescribed to treat recurrent Clostridioides difficile infection, which is an infectious disease, in human subjects. ¶¶ 66, 91-92 ’652 Patent, col. 24:38-41
...administering a pharmaceutical composition comprising a purified bacterial mixture of at least two live bacterial strains belonging to Clostridium clusters IV and/or XIVa... Vowst® is administered as a pharmaceutical composition and allegedly contains live bacteria from the genus Clostridium belonging to clusters IV and/or XIVa, sourced from human donors. ¶¶ 65, 67, 70, 73 ’652 Patent, col. 24:41-45
...wherein the bacterial strains are spore-forming bacteria... The accused product is described in its FDA-approved label as a "bacterial spore suspension" created by a process designed to isolate spores. ¶¶ 70, 72 ’652 Patent, col. 24:46-47
...and are isolated from a human. Vowst® is manufactured from human fecal matter sourced from qualified human donors. ¶70 ’652 Patent, col. 24:47-48
  • Identified Points of Contention:
    • Scope Questions: The analysis may focus on whether the Vowst® manufacturing process—treating fecal matter with ethanol and filtering—results in a "purified bacterial mixture" as required by the claim. The scope of "purified" will be a central question. Further, the complaint alleges the presence of Clostridium genera from specific clusters but may need to prove the presence of "at least two live bacterial strains" to meet the claim's requirement.

U.S. Patent 9,662,381 Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
A method of treating a human subject having an infectious disease... Vowst® is used to treat recurrent C. difficile infection in human adults. ¶¶ 66, 103 ’978 Patent, col. 118:14-17
...administering to the subject a pharmaceutical composition comprising a spore-forming fraction of human fecal matter... Vowst® is administered orally and is described as a "bacterial spore suspension" manufactured from human fecal matter. ¶¶ 67, 70, 72 ’978 Patent, col. 4:44-49
...wherein the composition induces proliferation and/or accumulation of regulatory T cells... The complaint alleges on information and belief that Vowst® has this function, supported by the assertion that it increases butyrate levels, which are known to promote Treg cell proliferation. ¶74 ’978 Patent, col. 3:50-54
...and wherein the composition is formulated for oral administration. Vowst® is provided in capsules for oral administration. ¶67 ’978 Patent, col. 15:23-44
  • Identified Points of Contention:
    • Technical Questions: A primary question will be evidentiary: what proof is required to demonstrate that Vowst® "induces proliferation and/or accumulation of regulatory T cells"? The complaint's reliance on an indirect mechanism (butyrate levels) may be challenged as insufficient to prove the claimed functional limitation is met in vivo.
    • Scope Questions: The term "spore-forming fraction" may be disputed. The court may need to determine whether the ethanol-based process for creating Vowst® produces a "fraction" within the meaning of the patent, particularly as the specification describes alternative methods like chloroform treatment (’978 Patent, col. 4:44-46).

V. Key Claim Terms for Construction

  • The Term: "purified bacterial mixture" (’652 Patent, Claim 1)

    • Context and Importance: This term is central to infringement of the ’652 Patent. The definition will determine whether the composition of Vowst®, derived from processed but inherently complex fecal matter, can be considered "purified."
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The specification describes isolating bacteria from a fecal sample, which could suggest that separation from the bulk of the fecal matter constitutes purification, even if the resulting mixture is not composed of pure isolates (’978 Patent, col. 12:58-67).
      • Evidence for a Narrower Interpretation: The claim uses "purified" and "mixture" together, which may imply a mixture of individually purified strains that are then combined. The patent describes experiments with defined bacterial strains, which could support an interpretation requiring a higher degree of purity than simple enrichment from a raw sample (’978 Patent, col. 32:15-24).

  • The Term: "induces proliferation and/or accumulation of regulatory T cells" (’381 Patent, Claim 1)

    • Context and Importance: This functional limitation is critical for infringement of the ’381 Patent and related patents. The dispute will likely center on the standard of proof required to show that the accused product performs this function.
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The patent describes the invention's "effect of inducing proliferation or accumulation of regulatory T cells" and notes this can be evaluated by administering the composition to an animal and measuring the ratio of Treg cells (’978 Patent, col. 11:13-17, 36-44). This may suggest that an observable increase in Treg cells is sufficient, without needing to prove the precise molecular pathway.
      • Evidence for a Narrower Interpretation: The patent's examples rely on direct measurement of Treg cells (e.g., via flow cytometry) in animal models to demonstrate the claimed effect (’978 Patent, FIG. 13, FIG. 50). This may support a requirement for direct clinical evidence of this specific biological activity in humans, as opposed to relying on indirect markers like butyrate levels.

VI. Other Allegations

  • Indirect Infringement: The complaint alleges induced infringement under 35 U.S.C. § 271(b) across all five asserted patents (Compl. ¶¶ 90, 102, 114, 129, 146). The allegations are based on Defendants' marketing, distributing, and providing prescribing information and instructions for Vowst®, which allegedly encourage and instruct physicians and patients to perform the patented methods of treatment (Compl. ¶¶ 84, 95). The complaint also alleges Seres induced Nestlé to infringe through their co-commercialization license agreement (Compl. ¶¶ 83, 120, 136, 153).
  • Willful Infringement: Willfulness is alleged for all asserted patents (Compl. ¶¶ 98, 109, 124, 141, 158). The allegations are based on alleged pre-suit knowledge of the patents-in-suit. The complaint alleges that Seres' 2023 10-K filing acknowledged awareness of "third-party patent families... that... could be construed to cover Vowst®" and that Seres filed an opposition against a related European patent of The University of Tokyo on April 25, 2017, demonstrating knowledge of the patent family years before the Vowst® launch (Compl. ¶86).

VII. Analyst’s Conclusion: Key Questions for the Case

  • A core issue will be one of definitional scope: does the Vowst® product, created by treating raw fecal matter with ethanol followed by filtration, meet the claimed requirements of a "purified bacterial mixture" (’652 Patent) or a "spore-forming fraction" (’381 Patent), or do these terms imply a higher degree of processing or separation than is used?
  • A key evidentiary question will be one of functional proof: what standard of evidence will be required to prove that Vowst® "induces proliferation and/or accumulation of regulatory T cells" as claimed? The case may turn on whether indirect biochemical evidence, such as increased butyrate levels, is sufficient to meet this burden, or if more direct clinical data showing an increase in the Treg cell population is necessary.
  • A third central question will concern willfulness and damages: given the complaint’s specific allegations of pre-launch knowledge, including references to SEC filings and European opposition proceedings, the court will likely scrutinize the timeline and extent of Defendants' awareness of the asserted patent family to determine whether any infringement was willful.