DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The reply filed October 15, 2025 overcomes the specification, claim objections, and the rejections under 35 U.S.C. § 112(b) and § 102 under Sutherland.
Upon further consideration of the prior art, prosecution is reopened to include claims 182 and 184 in the rejection under 35 U.S.C. § 101 and claim 1 in the § 102 rejection anticipated by Cunningham.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on October 15, 2025 has been considered by the examiner.
Specification
The new title, “Vaccines Comprising Proteins and/or Peptides of Methanobrevibacter gottschalkii”, has been entered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever 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, subject to the conditions and requirements of this title.
Claims 1, 3, 176, 178-180, 182, 183, 184, and 186-193 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature, without significantly more.
Instant claim 1 recites a vaccine comprising an adjuvant and a polypeptide or a fragment thereof of a Methanobrevibacter gottschalkii cell surface protein, wherein the polypeptide or fragment thereof, is recombinantly produced or chemically synthesized. Claim 183 also recites that the polypeptide or fragment thereof, is recombinantly produced. Claim 3 further requires Methanobrevibacter ruminantium. While recitation of “recombinantly produced” or “chemically synthesized” implies the deliberate production of the surface polypeptide or fragment thereof by the hand of man, the instant materials claimed are indistinguishable from a naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cell surface polypeptide or a fragment thereof and an adjuvant. Paragraph [0058] of the instant published disclosure, USPgPub 2025/0222082 (of record), states that Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium have been isolated from ruminants. In addition, Janssen et al. (Applied and Environmental Microbiology. June 2008; 74 (12): 3619-3625, of record) teach Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium exist abundantly in the rumen and exist freely in ruminal fluid (liquid recited in instant claim 182), see the paragraph bridging the columns on page 3619; “Abundant archaea in the rumen” on page 3620; Figure 1; Table 2; the second paragraph under, “Comparison with other methods” on page 3622; and the first paragraph under, “Archaeal community structure” on page 3622. Also see the second full paragraph on page 4 and Supplementary Fig. 1 of Henderson et al. (Scientific reports. 2015 Oct 9;5 (1): 14567, of record), which states:
Members of the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium clades were found in almost all samples, and were the two largest groups, accounting for 74% of all archaea.
All of the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium microorganisms possess cell surface proteins and fragments thereof, and bacterial products recited in claim 184(g), in nature. Regarding the recited adjuvant, Sutherland (USPgPub 2021/0261912, of record) explains the significance of preserving Methanobrevibacter archeae “pathogen-associated molecular patterns” (PAMPs) and “microbe-associated molecular patterns” (MAMPs), which attract innate immune system cells in paragraphs [0051-0071] and claims 1, 18, and 22. Ong et al. (Frontiers in cellular and infection microbiology. 2021 Oct 6; 11: 745016, of record) teach PAMPs are adjuvant components, see the title and abstract. Therefore, the presence of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium PAMPs and MAMPs satisfies the presence of at least one adjuvant (recited in instant claim 1) that is a bacterial product or derivative thereof (recited in instant claim 184(g)).
Similar to the fact pattern described in Myriad, the genetic information or genetic structure of the surface proteins, or fragments thereof, are not created or altered upon isolation from its native environment. Finding or discovering an important structure does not satisfy the §101 inquiry. Isolation by severing chemical bonds naturally linking the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins, or fragments thereof, from the remainder of the naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium, does not in itself provide a markedly different characteristic from any Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins, or fragments thereof, or nucleic acid encoding it, found in nature since there are no chemical changes resulting from the isolation. An assumption cannot be made the instant surface polypeptide or fragment thereof comprises any feature that is distinguishable from its naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface polypeptide as it exists in nature.
Instant claim 176 states that the at least one cell surface protein or a fragment thereof, comprises additional characteristics in the alternative and combination. Table 6G of the instant published disclosure lists cell surface proteins with the requisite characteristics claimed. Therefore, the least one cell surface protein or a fragment thereof, comprising additional characteristics in the alternative, and/or combination, are also products of nature. There is no evidence that the least one cell surface protein or a fragment thereof, comprising additional characteristics in the alternative and/or combination, have been recombinantly altered, mutated, or modified by the hand of man such that the nature or properties of the claimed surface polypeptide or fragment thereof, has changed.
Claims 179 and 180 recite quantities of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cells and proteins in the composition. However, specific quantities or amounts of natural materials present in a composition does not change the nature or properties of the natural products. Recited quantities do not indicate a structural or manipulative difference from the natural product to which the instant composition is compared. The instant Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cells and proteins remain indistinguishable from the naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cells and proteins.
Claims 178 states that the pharmaceutical composition comprises at least one carrier, at least one excipient. In paragraphs [0173 and 0174], “water” is listed as an exemplative diluent. The pharmaceutical carrier does not change the nature or properties of the combination of naturally-occurring materials claimed and does not render the instant composition different or distinguishable from the natural products.
Similar to the fact pattern described in Myriad, isolation of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium proteins and peptides are not created or altered upon isolation from its native environment. Finding or discovering an important structure does not satisfy the §101 inquiry. Isolation does not in itself provide a markedly different characteristic from any Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium proteins and peptides found in nature since there are no chemical changes resulting from the isolation. Therefore, the instant claims recite a natural phenomenon according to Step 2A in MPEP § 2106.04(II). The comparison between the material claimed and the material isolated from ruminants in the instant disclosure, Janssen et al., and Henderson et al. indicate that there are no differences in structure, function, or other characteristics. Therefore, the claimed Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium proteins and peptides are nature exception products. See Association for Molecular Pathology v. Myriad Genetics Inc., 569 U.S. 576, 589-90 (2013) (naturally occurring things are “products of nature” which cannot be patented). Accordingly, analysis must therefore proceed to Step 2A Prong Two.
Step 2A Prong Two requires eligibility analysis to evaluate whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. This evaluation is performed by (a) identifying whether there are any additional elements recited in the claim beyond the judicial exception, and (b) evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. The instant claims recite no additional element that distinguishes the instantly claimed Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium proteins and peptides from the naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium proteins and peptides. Instant claims 1, 3, 176, 178-182, 184, and 186 further require that the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cells proteins and peptides are encompassed in a “vaccine”. However, recitation of “vaccine” fails to meaningfully limit the claim because it is at best the equivalent of merely adding the words “apply it” to the judicial exception. The presence of a possible pharmaceutical carrier, vehicle, and/or excipient does not change the nature or properties of the naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium cells and proteins. Accordingly, recitation of a “vaccine” does not integrate the recited judicial exception into a practical application that is patent eligible pursuant to the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc. -U.S.—(June 13, 2013).
Instant claims 187-193 require the composition in a kit in various containers and doses.
As explained with respect to claims 1, 3, 176, 178-180, 182, and 186, isolated surface proteins and peptides and fragments thereof, of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium microorganisms are indistinguishable from naturally-occurring surface proteins and peptides and fragments thereof, of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium microorganisms. Recitation of a “kit” and containers therein, fail to meaningfully limit the claims because it is at best the equivalent of merely adding the words “apply it” to the judicial exception. There is no indication in the specification that placing the surface proteins from microorganisms in a generic container results in the microorganisms having any characteristics (structural, functional, or otherwise) that are different from the naturally occurring surface proteins in their natural state. Claims 192 and 193 recite dosage quantities within containers in the kit. Specific quantities or amounts of natural materials present in a composition does not change the nature or properties of the natural products. The instant protein products remain indistinguishable from the naturally-occurring protein products. The requirement of various quantities does not contribute to significantly more to the judicial exception. Therefore, the claimed population of surface proteins and peptides, and fragments thereof, of the microorganisms, does not have markedly different characteristics from what occurs in nature, and is a “product of nature” exception. Accordingly, recitation of a “kit” and containers and dosage amounts therein, does not integrate the recited judicial exception into a practical application that is patent eligible pursuant to the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc. -U.S.—(June 13, 2013).
In reply to the rejection of record, applicant points out that claim 1 is amended to include an adjuvant, recited in claim 183, according to the suggestion made on page 9 of the 7/15/2025 Office action.
Applicant’s amendment to the claim is noted. However, the requirements of an adjuvant suggested in the Office action, is that it changes the nature or properties of the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins. The presence of Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium PAMPs and MAMPs on surface proteins are adjuvant components, as taught by Sutherland and Ong et al. Therefore, the presence of an adjuvant (recited in instant claim 1) that is a bacterial product or derivative thereof (recited in instant claim 184(g)) is indistinguishable from naturally-occurring Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface polypeptides comprising PAMPs and MAMPs.
However, this rejection could be overcome if a Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface protein or fragment thereof, is combined with a substance that does change the nature or properties of the Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium protein products, such as combination with a lipid or saline, recited in claim 177 and/or one or more adjuvants, recited in (a)-(f), (h), and (i) of claim 183 or the adjuvants recited in instant claim 185.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 3, 176-178, 181-184, and 186 are rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Sutherland (USPgPub 2021/0261912 (of record)), as evidenced by Ong et al. (Frontiers in cellular and infection microbiology. 2021 Oct 6; 11: 745016 (of record)).
In reply to the rejection of record, applicant emphasizes that Sutherland does not teach or suggest a vaccine composition comprising a Methanobrevibacter gottschalkii polypeptide or fragment thereof that is recombinantly produced or chemically synthesized.
Applicant’s arguments and a review of the teachings of Sutherland have been fully considered, but are found unpersuasive. Paragraphs [0095 and 0096] of Sutherland teaches culturing the archaebacteria in “Methanobacterium Medium from the Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH) with or without a pelleting step, and the like”, which is recombinant technology, as recited in instant claims 1 and 183.
Sutherland anticipates a composition comprising inactivated or killed Methanobrevibacter archaebacteria cells in claim 18. Paragraph [0048] of Sutherland lists Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium encompassed by the genus of Methanobrevibacter archaebacteria cells recited in claim 18. Each microorganism of Sutherland comprises the surface proteins claimed in instant claims 1, 3, and 176, see Figure 2 and paragraphs [0070, 0071, and 0195]. Paragraph [0084] of Sutherland teach saline is a conventional liquid for suspending Methanobrevibacter archaebacteria cells, anticipating instant claims 177, 178, and 182. Paragraphs [0095, 0263, and 0267] of Sutherland anticipate lyophilized cells comprising surface proteins, as required by instant claim 181.
There is no structural difference between the claimed invention comprising Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins and the composition of Sutherland. Recitation of “vaccine” in the instant claims does not distinguish the instant composition from the composition of Sutherland because paragraph [0113] and claim 28 of Sutherland teaches that the composition of Methanobrevibacter archaebacteria cells is administered with a vaccine to improve immune system function and paragraph [0022] teaches that the population of Methanobrevibacter archaebacteria cells administered improves pathogen resistance and reduces intestinal inflammation. Also see claims 22-30. Increasing resistance to pathogens and therapeutically alleviating symptomology is naturally attributed to a “vaccine”. Therefore, the teachings of Sutherland anticipate instant intended use recited in instant claims 1, 3, 176-178, and 181-183.
Regarding the composition inducing an immune response in instant claim 186, the claim does not require actually using the vaccine composition in that way. Reducing methane production is not an additional structural limitation further characterizing the claimed product. See Catalina Mktg. Int'l, Inc. v. Coolsavings.com, Inc., 289 F.3d 801, 809 (Fed. Cir. 2002): “[T]he patentability of... composition claims depends on the claimed structure, not on the use or purpose of that structure.”). The claim is not drawn to a method of reducing methane emissions, it is are drawn to a product. There is nothing in the claims that requires the vaccine composition to have any specific function. There is no structural difference between the claimed invention comprising Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins and the composition of Sutherland comprising Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium surface proteins. Therefore, the composition of Sutherland anticipates instant claim 186.
While Sutherland does not mention “an adjuvant”, per se, as required by instant claims 1 and 184, Sutherland explains the significance of preserving “pathogen-associated molecular patterns” (PAMPs) and “microbe-associated molecular patterns” (MAMPs), i.e., bacterial products or a derivative thereof, recited in instant claim 184(g), which attracts innate immune system cells in paragraphs [0051-0071] and claims 1, 18, and 22. Ong et al. teach PAMPs are adjuvant components, see the title and abstract. Therefore, the preservation of PAMPs and MAMPs on the inactivated Methanobrevibacter of Sutherland provide an adjuvanting immune stimulating complex, recited in instant claims 1 and 184.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 179, 180, and 185 remain rejected under 35 U.S.C. 103 as being unpatentable over Sutherland, as evidenced by Ong et al., supra and Wright et al. (Vaccine. 2004; 22: 3976-3985) for reasons of record. All references are of record.
In reply to the rejection of record, applicant emphasizes that Sutherland does not teach or suggest a vaccine composition comprising a Methanobrevibacter gottschalkii polypeptide or fragment thereof that is recombinantly produced or chemically synthesized and Wright et al. do not cure the deficiency.
Applicant’s arguments have been fully considered, but are found unpersuasive since there are no deficiencies for Wright et al. to cure. Paragraphs [0095 and 0096] of Sutherland teaches culturing the archaebacteria in “Methanobacterium Medium from the Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH) with or without a pelleting step, and the like”, which is recombinant technology.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected and claims 187-193 remain rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Cunningham (WO 2012/142605, of record).
In reply to the rejection of record, applicant emphasizes that Cunningham does not teach or suggest a vaccine composition comprising a Methanobrevibacter gottschalkii polypeptide or fragment thereof that is recombinantly produced or chemically synthesized.
Applicant’s arguments and a review of the teachings of Cunningham have been fully considered, but are found unpersuasive. The last paragraph on page 6 of Cunningham teaches culturing and freeze-drying the microbial agents, which is recombinant technology, as recited in instant claim 1.
Claim 197 remains rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by is anticipated Cunningham supra, as evidenced by Sutherland (USPgPub 2021/0261912) and Ong et al. (Frontiers in cellular and infection microbiology. 2021 Oct 6; 11: 745016). All references of record.
In reply to the rejection of record, applicant emphasizes that Cunningham does not teach or suggest a vaccine composition comprising a Methanobrevibacter gottschalkii polypeptide or fragment thereof that is recombinantly produced or chemically synthesized.
Applicant’s arguments and a review of the teachings of Cunningham have been fully considered, but are found unpersuasive. The last paragraph on page 6 of Cunningham teaches culturing and freeze-drying the microbial agents, which is recombinant technology, as recited in instant claim 1.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 195-196 remains rejected under 35 U.S.C. 103 as being unpatentable over Cunningham supra and Fox et al. (Therapeutic Advances in Vaccines. 2013; 1 (1): 7-20).
In reply to the rejection of record, applicant asserts that Fox et al. do not cure the deficiencies of Cunningham.
Applicant’s arguments have been fully considered, but are found unpersuasive since there are no deficiencies for Fox et al. to cure. The last paragraph on page 6 of Cunningham teaches culturing and freeze-drying the microbial agents, which is recombinant technology, as recited in instant claim 1.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Khanum et al. (Frontiers in Microbiology. August 2022; 13: 918111) describe vaccinating sheep with whole-cell preparations of various Methanobrevibacter spp. in “Production of antisera…” on page 3. Khanum et al. demonstrate antibodies against some ruminant methanogen surface proteins cross-react with other methanogen species surface proteins in Table 2 and Figures 1-5. Khanum et al. proposes to develop a broad-spectrum vaccine to reduce methane emissions in livestock in the abstract and Discussion sections.
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/Shanon A. Foley/ Primary Examiner, Art Unit 1671